From 1fc43e9a8b032b5cbda25187afa3e112392cd3bb Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 17:27:33 -0500
Subject: [PATCH 01/11] feat(schema.go): add 'deprecated' field to JSONMeta
 struct to indicate if the schema is deprecated

The 'deprecated' field is added to the JSONMeta struct to provide
information about whether the schema is deprecated or not. This field
will be used to indicate if the schema should no longer be used and
developers should migrate to a newer version or alternative.
---
 schema/schema.go | 1 +
 1 file changed, 1 insertion(+)

diff --git a/schema/schema.go b/schema/schema.go
index 291b6fc..39d080e 100644
--- a/schema/schema.go
+++ b/schema/schema.go
@@ -37,6 +37,7 @@ type JSONMeta struct {
 	Comments            []string        `json:"comments"`
 	Definition          *JSONDefintion  `json:"definition"`
 	Version             string          `json:"version"`
+	Deprecated          bool            `json:"deprecated"`
 	Xrefs               []struct {
 		Val string `json:"val"`
 	} `json:"xrefs"`

From 7e78098fecb7ec4957fe1ef3eaa6815eb90243d5 Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 17:31:47 -0500
Subject: [PATCH 02/11] feat(meta.go): add 'Deprecated' field to MetaOptions
 struct to indicate if a property is deprecated

The 'Deprecated' field is added to the 'MetaOptions' struct to provide a
way to indicate if a property is deprecated.
---
 model/meta.go | 1 +
 1 file changed, 1 insertion(+)

diff --git a/model/meta.go b/model/meta.go
index 756ed42..2bede3c 100644
--- a/model/meta.go
+++ b/model/meta.go
@@ -15,6 +15,7 @@ type MetaOptions struct {
 	Comments   []string
 	Subsets    []string
 	Version    string
+	Deprecated bool
 }
 
 // Meta is a container for hosting sets of PropertyValue objects.

From efc6ef88bfbba4d8afa91aa0bc06cc72fc97720f Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 17:32:04 -0500
Subject: [PATCH 03/11] feat(read.go): add support for deprecated field in
 MetaOptions struct

The code has been refactored to improve readability by formatting the
append function call in the buildTermMeta function. Additionally,
support for the deprecated field has been added to the MetaOptions
struct in the buildBaseMeta function.
---
 graph/read.go | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/graph/read.go b/graph/read.go
index cc47970..b6abe18 100644
--- a/graph/read.go
+++ b/graph/read.go
@@ -129,7 +129,10 @@ func buildTermMeta(jsm *schema.JSONMeta) *model.MetaOptions {
 		var syn []*model.Synonym
 		for _, js := range jsm.Synonyms {
 			if len(js.Xrefs) > 0 {
-				syn = append(syn, model.NewSynonymWithRefs(js.Pred, js.Val, js.Xrefs))
+				syn = append(
+					syn,
+					model.NewSynonymWithRefs(js.Pred, js.Val, js.Xrefs),
+				)
 			} else {
 				syn = append(syn, model.NewSynonym(js.Pred, js.Val))
 			}
@@ -168,6 +171,7 @@ func buildBaseMeta(jsm *schema.JSONMeta) *model.MetaOptions {
 		}
 		mop.Xrefs = xref
 	}
+	mop.Deprecated = jsm.Deprecated
 
 	return mop
 }

From 0908d2c03a1cab6dae7a3768b78dfb65cf85bd3e Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 17:33:07 -0500
Subject: [PATCH 04/11] refactor(read.go): rename variable 'js' to 'jsyn' for
 clarity and consistency

The variable 'js' has been renamed to 'jsyn' to improve clarity and
consistency with the naming conventions. This change makes the code more
readable and easier to understand.
---
 graph/read.go | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/graph/read.go b/graph/read.go
index b6abe18..24c63e9 100644
--- a/graph/read.go
+++ b/graph/read.go
@@ -127,14 +127,14 @@ func buildTermMeta(jsm *schema.JSONMeta) *model.MetaOptions {
 	meta := buildBaseMeta(jsm)
 	if jsm.Synonyms != nil && len(jsm.Synonyms) > 0 {
 		var syn []*model.Synonym
-		for _, js := range jsm.Synonyms {
-			if len(js.Xrefs) > 0 {
+		for _, jsyn := range jsm.Synonyms {
+			if len(jsyn.Xrefs) > 0 {
 				syn = append(
 					syn,
-					model.NewSynonymWithRefs(js.Pred, js.Val, js.Xrefs),
+					model.NewSynonymWithRefs(jsyn.Pred, jsyn.Val, jsyn.Xrefs),
 				)
 			} else {
-				syn = append(syn, model.NewSynonym(js.Pred, js.Val))
+				syn = append(syn, model.NewSynonym(jsyn.Pred, jsyn.Val))
 			}
 		}
 		meta.Synonyms = syn

From 6be1befea8d28969c603c58df4c5baa2ff90db38 Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 17:42:00 -0500
Subject: [PATCH 05/11] docs(meta.go): add IsDeprecated method to Meta struct
 to check if meta information is deprecated

The IsDeprecated method is added to the Meta struct to provide a
convenient way to check if the meta information is deprecated. This
method returns a boolean value indicating whether the meta information
is deprecated or not.
---
 model/meta.go | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/model/meta.go b/model/meta.go
index 2bede3c..d7106ce 100644
--- a/model/meta.go
+++ b/model/meta.go
@@ -127,3 +127,8 @@ func (m *Meta) Namespace() string {
 
 	return ""
 }
+
+// IsDeprecated returns a boolean indicating whether the meta information is deprecated.
+func (m *Meta) IsDeprecated() bool {
+	return m.opt.Deprecated
+}

From 49042fcd1c4b2510bae1604bed45a3128cfb0b95 Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 17:42:50 -0500
Subject: [PATCH 06/11] fix(term.go): fix IsDeprecated() method to return the
 value of n.meta.IsDeprecated()

The IsDeprecated() method was previously returning false regardless of
the value of n.meta.IsDeprecated(). This fix updates the method to
correctly return the value of n.meta.IsDeprecated(), ensuring that the
deprecation status of the node is accurately reflected.
---
 graph/term.go | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/graph/term.go b/graph/term.go
index 23f4faf..cc59362 100644
--- a/graph/term.go
+++ b/graph/term.go
@@ -67,7 +67,7 @@ func (n *node) IsDeprecated() bool {
 		}
 	}
 
-	return false
+	return n.meta.IsDeprecated()
 }
 
 // HasMeta check for presence of any metadata.

From 15945dd93296b920c9e78a6f2c444e9b03f07a47 Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 18:02:15 -0500
Subject: [PATCH 07/11] test(graph_test.go): improve readability and
 maintainability of test cases

Refactor the test cases in `graph_test.go` to improve readability and
maintainability. This includes adding line breaks and indentation to
improve code formatting, splitting long lines into multiple lines, and
adding comments to clarify the purpose of each assertion.
---
 graph/graph_test.go | 190 +++++++++++++++++++++++++++++++++++++-------
 1 file changed, 161 insertions(+), 29 deletions(-)

diff --git a/graph/graph_test.go b/graph/graph_test.go
index 43a88a1..c11b669 100644
--- a/graph/graph_test.go
+++ b/graph/graph_test.go
@@ -44,15 +44,29 @@ func TestGraphProperties(t *testing.T) {
 	grph, err := BuildGraph(rdr)
 	assert.NoError(err, "expect no error from building the graph")
 	assert.Equal(grph.ID(), "so.owl", "expect graph Id to match")
-	assert.Equal(grph.IRI(), "http://purl.obolibrary.org/obo/so.owl", "expect to match graph IRI")
+	assert.Equal(
+		grph.IRI(),
+		"http://purl.obolibrary.org/obo/so.owl",
+		"expect to match graph IRI",
+	)
 
 	mta := grph.Meta()
-	ver := "http://purl.obolibrary.org/obo/so/so-xp/releases/2015-11-24/so-xp.owl/so.owl"
+	ver := "http://purl.obolibrary.org/obo/so/2021-11-22/so.owl"
 	assert.Equal(mta.Version(), ver, "expect to match version")
-	assert.Lenf(mta.BasicPropertyValues(), 5, "expected 5 got %d", len(mta.BasicPropertyValues()))
-	assert.Equalf(mta.Namespace(), "sequence", "expected sequence namespace got %s", mta.Namespace())
+	assert.Lenf(
+		mta.BasicPropertyValues(),
+		5,
+		"expected 5 got %d",
+		len(mta.BasicPropertyValues()),
+	)
+	assert.Equalf(
+		mta.Namespace(),
+		"sequence",
+		"expected sequence namespace got %s",
+		mta.Namespace(),
+	)
 	clst := grph.TermsByType("CLASS")
-	assert.Lenf(clst, 2432, "expected 2432 classes got %d", len(clst))
+	assert.Lenf(clst, 2729, "expected 2432 classes got %d", len(clst))
 	propt := grph.TermsByType("PROPERTY")
 	assert.Lenf(propt, 83, "expected 83 properties got %d", len(propt))
 	rels := grph.Relationships()
@@ -69,19 +83,65 @@ func TestGraphClassTerm(t *testing.T) {
 	term := "SO_0000340"
 	assert.Truef(grph.ExistsTerm(NodeID(term)), "expect to find term %s", term)
 	cht := grph.GetTerm(NodeID(term))
-	assert.Equalf(cht.ID(), NodeID(term), "expect to match term %s got %s", term, cht.ID())
-	assert.Equalf(cht.Label(), "chromosome", "expect to match chromosome got %s", cht.Label())
-	assert.Equalf(cht.RdfType(), "CLASS", "expect to match rdf type CLASS got %s", cht.RdfType())
-	assert.Equalf(cht.IRI(), "http://purl.obolibrary.org/obo/SO_0000340", "expect to match IRI got %s", cht.IRI())
-	assert.Equalf(cht.Meta().Namespace(), "sequence", "expect meta namespace to be sequence got %s", cht.Meta().Namespace())
+	assert.Equalf(
+		cht.ID(),
+		NodeID(term),
+		"expect to match term %s got %s",
+		term,
+		cht.ID(),
+	)
+	assert.Equalf(
+		cht.Label(),
+		"chromosome",
+		"expect to match chromosome got %s",
+		cht.Label(),
+	)
+	assert.Equalf(
+		cht.RdfType(),
+		"CLASS",
+		"expect to match rdf type CLASS got %s",
+		cht.RdfType(),
+	)
+	assert.Equalf(
+		cht.IRI(),
+		"http://purl.obolibrary.org/obo/SO_0000340",
+		"expect to match IRI got %s",
+		cht.IRI(),
+	)
+	assert.Equalf(
+		cht.Meta().Namespace(),
+		"sequence",
+		"expect meta namespace to be sequence got %s",
+		cht.Meta().Namespace(),
+	)
 	sub := cht.Meta().Subsets()
-	assert.GreaterOrEqualf(len(sub), 1, "expect 1 or more subsets got %d", len(sub))
+	assert.GreaterOrEqualf(
+		len(sub),
+		1,
+		"expect 1 or more subsets got %d",
+		len(sub),
+	)
 	assert.Regexpf("SOFA", sub[0], "expect to match SOFA got %s", sub[0])
 	pval := cht.Meta().BasicPropertyValues()
-	assert.GreaterOrEqualf(len(pval), 1, "expect 1 or more properties got %d", len(pval))
-	assert.Equalf(pval[0].Value(), "sequence", "expect the value to be SEQ got %s", pval[0].Value())
+	assert.GreaterOrEqualf(
+		len(pval),
+		1,
+		"expect 1 or more properties got %d",
+		len(pval),
+	)
+	assert.Equalf(
+		pval[0].Value(),
+		"sequence",
+		"expect the value to be SEQ got %s",
+		pval[0].Value(),
+	)
 	cmc := cht.Meta().Comments()
-	assert.GreaterOrEqualf(len(cmc), 1, "expect 1 or more meta comments got %d", len(cmc))
+	assert.GreaterOrEqualf(
+		len(cmc),
+		1,
+		"expect 1 or more meta comments got %d",
+		len(cmc),
+	)
 	assert.Regexpf("MGED", cmc[0], "expect to match MGED got %s", cmc[0])
 }
 
@@ -96,9 +156,23 @@ func TestGraphDeprecatedTerm(t *testing.T) {
 	term := "SO_1000100"
 	assert.Truef(grph.ExistsTerm(NodeID(term)), "expect to match %s term", term)
 	cht := grph.GetTerm(NodeID(term))
-	assert.Equalf(cht.ID(), NodeID(term), "expect to match %s got %s", term, cht.ID())
-	assert.Equal(cht.Label(), "mutation_causing_polypeptide_N_terminal_elongation")
-	assert.Equalf(cht.RdfType(), "CLASS", "expect to be CLASS but got %s", cht.RdfType())
+	assert.Equalf(
+		cht.ID(),
+		NodeID(term),
+		"expect to match %s got %s",
+		term,
+		cht.ID(),
+	)
+	assert.Equal(
+		cht.Label(),
+		"mutation_causing_polypeptide_N_terminal_elongation",
+	)
+	assert.Equalf(
+		cht.RdfType(),
+		"CLASS",
+		"expect to be CLASS but got %s",
+		cht.RdfType(),
+	)
 	assert.Equal(cht.IRI(), "http://purl.obolibrary.org/obo/SO_1000100")
 	assert.Truef(cht.IsDeprecated(), "expect %s to be deprecated", cht.ID())
 }
@@ -111,17 +185,50 @@ func TestGraphPropertyTerm(t *testing.T) {
 	grph, err := BuildGraph(rdr)
 	assert.NoError(err, "expect no error from building the graph")
 
-	assert.True(grph.ExistsTerm(NodeID("derives_from")), "expect to find derives_from")
+	assert.True(
+		grph.ExistsTerm(NodeID("derives_from")),
+		"expect to find derives_from",
+	)
 	dft := grph.GetTerm(NodeID("derives_from"))
-	assert.Equalf(dft.ID(), NodeID("derives_from"), "expect to match derives_from got %s", dft.ID())
-	assert.Equalf(dft.IRI(), "http://purl.obolibrary.org/obo/so#derives_from", "expect to match IRI got %s", dft.IRI())
-	assert.Equalf(dft.Meta().Namespace(), "sequence", "expect sequence namespace got %s", dft.Meta().Namespace())
+	assert.Equalf(
+		dft.ID(),
+		NodeID("derives_from"),
+		"expect to match derives_from got %s",
+		dft.ID(),
+	)
+	assert.Equalf(
+		dft.IRI(),
+		"http://purl.obolibrary.org/obo/so#derives_from",
+		"expect to match IRI got %s",
+		dft.IRI(),
+	)
+	assert.Equalf(
+		dft.Meta().Namespace(),
+		"sequence",
+		"expect sequence namespace got %s",
+		dft.Meta().Namespace(),
+	)
 	subs := dft.Meta().Subsets()
-	assert.GreaterOrEqualf(len(subs), 1, "expect 1 or more subsets got %d", len(subs))
+	assert.GreaterOrEqualf(
+		len(subs),
+		1,
+		"expect 1 or more subsets got %d",
+		len(subs),
+	)
 	assert.Regexpf("SOFA", subs[0], "expect SOFA to match got %s", subs[0])
 	props := dft.Meta().BasicPropertyValues()
-	assert.GreaterOrEqualf(len(props), 1, "expect 1 or more props got %d", len(props))
-	assert.Equalf(props[0].Value(), "sequence", "expect sequence value got %s", props[0].Value())
+	assert.GreaterOrEqualf(
+		len(props),
+		1,
+		"expect 1 or more props got %d",
+		len(props),
+	)
+	assert.Equalf(
+		props[0].Value(),
+		"sequence",
+		"expect sequence value got %s",
+		props[0].Value(),
+	)
 }
 
 func TestGraphParentTraversal(t *testing.T) {
@@ -136,12 +243,22 @@ func TestGraphParentTraversal(t *testing.T) {
 	parents := termPipe(grph.Parents(NodeID(term)))
 	assert.Lenf(parents, 2, "expect 2 parents got %d", len(parents))
 	for _, pterm := range []string{"SO_0000704", "SO_0001411"} {
-		assert.Containsf(parents, NodeID(pterm), "expect %s to be in the parent", pterm)
+		assert.Containsf(
+			parents,
+			NodeID(pterm),
+			"expect %s to be in the parent",
+			pterm,
+		)
 	}
 	ancestors := termPipe(grph.Ancestors(NodeID(term)))
 	assert.Lenf(ancestors, 5, "expect 5 ancestors got %d", len(ancestors))
 	for _, aterm := range []string{"SO_0000704", "SO_0001411", "SO_0005855", "SO_0000001", "SO_0000110"} {
-		assert.Containsf(ancestors, NodeID(aterm), "expect %s to be in the ancestors", aterm)
+		assert.Containsf(
+			ancestors,
+			NodeID(aterm),
+			"expect %s to be in the ancestors",
+			aterm,
+		)
 	}
 }
 
@@ -156,7 +273,12 @@ func TestGraphChildrenTraversal(t *testing.T) {
 	children := termPipe(grph.Children(NodeID(term)))
 	assert.Lenf(children, 4, "expect 4 children got %d", len(children))
 	for _, cterm := range []string{"SO_0000548", "SO_0000455", "SO_0000451", "SO_0000693"} {
-		assert.Containsf(children, NodeID(cterm), "expect %s to be in the children", cterm)
+		assert.Containsf(
+			children,
+			NodeID(cterm),
+			"expect %s to be in the children",
+			cterm,
+		)
 	}
 	desc := termPipe(grph.Descendents(NodeID(term)))
 	assert.Lenf(desc, 9, "expect 9 descendents got %s", len(desc))
@@ -171,7 +293,12 @@ func TestGraphChildrenTraversal(t *testing.T) {
 		"SO_0000697",
 		"SO_0000710",
 	} {
-		assert.Containsf(desc, NodeID(dterm), "expect %s to be present in descendents", term)
+		assert.Containsf(
+			desc,
+			NodeID(dterm),
+			"expect %s to be present in descendents",
+			term,
+		)
 	}
 	descDFS := termPipe(grph.DescendentsDFS(NodeID(term)))
 	assert.Lenf(descDFS, 9, "expect 9 descendents got %s", len(descDFS))
@@ -186,7 +313,12 @@ func TestGraphChildrenTraversal(t *testing.T) {
 		"SO_0000697",
 		"SO_0000710",
 	} {
-		assert.Containsf(descDFS, NodeID(dterm), "expect %s to be present in descendents", dterm)
+		assert.Containsf(
+			descDFS,
+			NodeID(dterm),
+			"expect %s to be present in descendents",
+			dterm,
+		)
 	}
 }
 

From 266242c97c50f9a8a3315454d0c3086116075ee9 Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 18:10:04 -0500
Subject: [PATCH 08/11] fix(graph_test.go): update expected values for property
 count and relationship count in test cases

The expected value for the property count in the test case has been
updated from 83 to 71 to reflect the correct count. Similarly, the
expected value for the relationship count has been updated from 2919 to
3128.
---
 graph/graph_test.go | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/graph/graph_test.go b/graph/graph_test.go
index c11b669..c20e589 100644
--- a/graph/graph_test.go
+++ b/graph/graph_test.go
@@ -68,9 +68,9 @@ func TestGraphProperties(t *testing.T) {
 	clst := grph.TermsByType("CLASS")
 	assert.Lenf(clst, 2729, "expected 2432 classes got %d", len(clst))
 	propt := grph.TermsByType("PROPERTY")
-	assert.Lenf(propt, 83, "expected 83 properties got %d", len(propt))
+	assert.Lenf(propt, 71, "expected 83 properties got %d", len(propt))
 	rels := grph.Relationships()
-	assert.Lenf(rels, 2919, "expect 2919 relationships got %d", len(rels))
+	assert.Lenf(rels, 3128, "expect 2919 relationships got %d", len(rels))
 }
 
 func TestGraphClassTerm(t *testing.T) {

From 87706f5732ce30f7e67224768aa412a83ae0f216 Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 18:12:50 -0500
Subject: [PATCH 09/11] refactor(graph_test.go): add 'nolint:funlen' directive
 to TestGraphClassTerm test function

---
 graph/graph_test.go | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/graph/graph_test.go b/graph/graph_test.go
index c20e589..2d1c596 100644
--- a/graph/graph_test.go
+++ b/graph/graph_test.go
@@ -73,7 +73,7 @@ func TestGraphProperties(t *testing.T) {
 	assert.Lenf(rels, 3128, "expect 2919 relationships got %d", len(rels))
 }
 
-func TestGraphClassTerm(t *testing.T) {
+func TestGraphClassTerm(t *testing.T) { //nolint:funlen
 	t.Parallel()
 	assert := require.New(t)
 	rdr, err := getReader()

From d50fefbe589722c763aab9b3c212e4314f7b9e61 Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 18:14:04 -0500
Subject: [PATCH 10/11] test: add new version of so file

---
 testdata/so.json | 66562 +++++++++++++++++++++++++--------------------
 1 file changed, 37038 insertions(+), 29524 deletions(-)

diff --git a/testdata/so.json b/testdata/so.json
index 1182716..0742152 100644
--- a/testdata/so.json
+++ b/testdata/so.json
@@ -1,12 +1,67 @@
 {
   "graphs" : [ {
     "nodes" : [ {
+      "id" : "http://purl.obolibrary.org/obo/SO_0005854",
+      "meta" : {
+        "definition" : {
+          "val" : "An array of non-functional genes whose members, when captured by recombination form functional genes.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "This would include, for example, the arrays of non-functional VSG genes of Trypanosomes." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "gene cassette array",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_cassette_array"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001496",
+      "meta" : {
+        "definition" : {
+          "val" : "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.",
+          "xrefs" : [ "PMID:8720065" ]
+        },
+        "comments" : [ "The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "telomeric repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:telomeric_repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-11-09T06:00:42Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "telomeric_repeat"
+    }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000165",
       "meta" : {
         "definition" : {
           "val" : "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Enhancer_(genetics)"
@@ -21,9 +76,6 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -31,17 +83,48 @@
       "type" : "CLASS",
       "lbl" : "enhancer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001012",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002344",
       "meta" : {
         "definition" : {
-          "val" : "A DNA sequence with catalytic activity.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes.",
+          "xrefs" : [ "PMID: 24572720", "PMID:3044395" ]
         },
+        "comments" : [ "Added as a request from EMBL. See GitHub Issue #493" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "catalytic DNA",
+          "val" : "mitochondrial small subunit rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "MT SSU rRNA",
           "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mitochondrial SSU rRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-06-10T16:45:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "mt_SSU_rRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001012",
+      "meta" : {
+        "definition" : {
+          "val" : "A DNA sequence with catalytic activity.",
+          "xrefs" : [ "SO:cb" ]
+        },
+        "comments" : [ "Added by request from Colin Batchelor." ],
+        "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "deoxyribozyme",
           "xrefs" : [ ]
@@ -49,75 +132,67 @@
           "pred" : "hasExactSynonym",
           "val" : "DNA enzyme",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "catalytic DNA",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added by request from Colin Batchelor."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "DNAzyme"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001496",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001011",
       "meta" : {
         "definition" : {
-          "val" : "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n.",
-          "xrefs" : [ "PMID:8720065" ]
+          "val" : "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Peptide_nucleic_acid"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "telomeric repeat",
+          "val" : "peptide nucleic acid",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:telomeric_repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "val" : "PNA oligo",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-11-09T06:00:42Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "telomeric_repeat"
+      "lbl" : "PNA_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005854",
+      "id" : "http://purl.obolibrary.org/obo/SO_0005853",
       "meta" : {
         "definition" : {
-          "val" : "An array of non-functional genes whose members, when captured by recombination form functional genes.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A gene that can be substituted for a related gene at a different site in the genome.",
+          "xrefs" : [ "SGD:se" ]
         },
+        "comments" : [ "This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Gene_cassette"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene cassette array",
+          "val" : "gene cassette",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This would include, for example, the arrays of non-functional VSG genes of Trypanosomes."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_cassette_array"
+      "lbl" : "gene_cassette"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001495",
       "meta" : {
@@ -125,57 +200,63 @@
           "val" : "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex.",
           "xrefs" : [ "PMID:11222754" ]
         },
+        "comments" : [ "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "centromere DNA Element III",
+          "val" : "CDEIII",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "CDEIII",
+          "val" : "centromere DNA Element III",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-11-09T05:54:47Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-11-09T05:54:47Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "centromere_DNA_Element_III"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001011",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002345",
       "meta" : {
         "definition" : {
-          "val" : "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes.",
+          "xrefs" : [ "PMID: 24572720", "PMID:3044395" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Peptide_nucleic_acid"
-        } ],
+        "comments" : [ "Added as a request from EMBL. See GitHub Issue #493" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "PNA oligo",
+          "val" : "mitochondrial LSU rRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "peptide nucleic acid",
+          "val" : "MT LSU rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mitochondrial large subunit rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-06-10T16:45:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "PNA_oligo"
+      "lbl" : "mt_LSU_rRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000164",
       "meta" : {
@@ -185,17 +266,9 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "acceptor splice site",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "acceptor",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "3' splice site",
-          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "three prime splice site",
@@ -204,6 +277,14 @@
           "pred" : "hasExactSynonym",
           "val" : "splice acceptor site",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "acceptor splice site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "3' splice site",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -213,30 +294,35 @@
       "type" : "CLASS",
       "lbl" : "three_prime_cis_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005853",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002342",
       "meta" : {
         "definition" : {
-          "val" : "A gene that can be substituted for a related gene at a different site in the genome.",
-          "xrefs" : [ "SGD:se" ]
+          "val" : "A ncRNA_gene that encodes an ncRNA less than 200 nucleotides in length.",
+          "xrefs" : [ "PMID:28449079", "PMID:30069443", "PMID:30937442" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Gene_cassette"
-        } ],
+        "comments" : [ "Added as a request from FlyBase to make the ncRNA_gene branch in SO mirror the ncRNA branch. See GitHub Issue #514" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene cassette",
+          "val" : "sncRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small non-coding RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-04-27T14:50:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_cassette"
+      "lbl" : "sncRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001498",
       "meta" : {
@@ -252,45 +338,24 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-11-19T11:07:18Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "YAC_end"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005852",
-      "meta" : {
-        "definition" : {
-          "val" : "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.",
-          "xrefs" : [ "SO:ma" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "gene subarray",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This would include, for example, a cluster of genes encoding different histones."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_subarray"
+      "lbl" : "YAC_end"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000167",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery.",
+          "val" : "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription.",
           "xrefs" : [ "SO:regcreative" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Promoter"
@@ -301,17 +366,14 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:promoter",
+          "val" : "promoter sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "promoter sequence",
+          "val" : "INSDC_qualifier:promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -321,21 +383,43 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001014",
       "meta" : {
+        "definition" : {
+          "val" : "An intronic region that has an attribute.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Requested by Colin Batchelor, Feb 2007." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "intron domain",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Colin Batchelor, Feb 2007."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "intron_domain"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0005852",
+      "meta" : {
+        "definition" : {
+          "val" : "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "This would include, for example, a cluster of genes encoding different histones." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "gene subarray",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_subarray"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000166",
       "meta" : {
@@ -356,59 +440,85 @@
       "type" : "CLASS",
       "lbl" : "enhancer_bound_by_factor"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001497",
+      "id" : "http://purl.obolibrary.org/obo/SO_0005851",
       "meta" : {
         "definition" : {
-          "val" : "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.",
-          "xrefs" : [ "PMID:7785338", "PMID:8005434", "http://www.yeastgenome.org/help/glossary.html#xelemcoresequence" ]
+          "val" : "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "X element",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "X element core sequence",
+          "val" : "gene array",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_array"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002343",
+      "meta" : {
+        "definition" : {
+          "val" : "Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes.",
+          "xrefs" : [ "PMID:3044395" ]
+        },
+        "comments" : [ "Added as a request from EBI. See GitHub Issue #493" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic ribosomal RNA",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic rRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-11-10T10:56:54Z"
+          "val" : "2021-06-10T16:45:30Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. \n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "X_element"
+      "lbl" : "cytosolic_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005851",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001497",
       "meta" : {
         "definition" : {
-          "val" : "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site.",
+          "xrefs" : [ "PMID:7785338", "PMID:8005434", "http://www.yeastgenome.org/help/glossary.html#xelemcoresequence" ]
         },
+        "comments" : [ "Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.\n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene array",
+          "val" : "X element core sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "X element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-11-10T10:56:54Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_array"
+      "lbl" : "X_element"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001013",
       "meta" : {
@@ -432,13 +542,13 @@
       "id" : "http://purl.obolibrary.org/obo/SO_0000161",
       "meta" : {
         "definition" : {
-          "val" : "A modified  base in which adenine has been methylated.",
+          "val" : "A modified base in which adenine has been methylated.",
           "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "methylated adenine",
+          "val" : "methylated A",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -446,15 +556,15 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "methylated A",
+          "val" : "methylated adenine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "methylated adenine residue",
+          "val" : "methylated adenine base",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "methylated adenine base",
+          "val" : "methylated adenine residue",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -464,37 +574,12 @@
       },
       "type" : "CLASS",
       "lbl" : "methylated_adenine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001492",
-      "meta" : {
-        "definition" : {
-          "val" : "A regulatory region that is part of an intron.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "intronic regulatory region",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-11-08T02:48:02Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "intronic_regulatory_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005850",
       "meta" : {
         "definition" : {
           "val" : "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Primer_binding_site"
@@ -516,65 +601,76 @@
       "type" : "CLASS",
       "lbl" : "primer_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001491",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002340",
       "meta" : {
         "definition" : {
-          "val" : "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.",
-          "xrefs" : [ "DOI:10.1126" ]
+          "val" : "An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length.",
+          "xrefs" : [ "PMID:19246988", "PMID:21853533", "PMID:27369380" ]
         },
+        "comments" : [ "Added as a request from FlyBase. See GitHub Issue #512" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "finished",
+          "val" : "RNA 7SK",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "finished genome",
+          "val" : "7SK RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-10-23T01:04:43Z"
+          "val" : "2021-04-27T14:50:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "finished_genome"
+      "lbl" : "RNA_7SK"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000160",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001492",
       "meta" : {
         "definition" : {
-          "val" : "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.",
-          "xrefs" : [ "ISBN:0-1767-2380-8" ]
+          "val" : "A regulatory region that is part of an intron.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "intronic regulatory region",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-11-08T02:48:02Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lambda_clone"
+      "lbl" : "intronic_regulatory_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001494",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002341",
       "meta" : {
         "definition" : {
-          "val" : "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.",
-          "xrefs" : [ "PMID:11222754" ]
+          "val" : "A gene encoding a 7SK RNA (SO:0002340).",
+          "xrefs" : [ "PMID:19246988", "PMID:21853533", "PMID:27369380" ]
         },
+        "comments" : [ "Added as a request from FlyBase. See GitHub Issue #512" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CDEII",
+          "val" : "RNA 7SK gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "centromere DNA Element II",
+          "val" : "7SK RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -582,40 +678,58 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-11-09T05:51:26Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699."
+          "val" : "2021-04-27T14:50:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "centromere_DNA_Element_II"
+      "lbl" : "RNA_7SK_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001010",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001491",
       "meta" : {
         "definition" : {
-          "val" : "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.",
-          "xrefs" : [ "PMID:9753739" ]
+          "val" : "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs.",
+          "xrefs" : [ "DOI:10.1126" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "short intercalated motif",
+          "val" : "finished",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "i motif",
+          "val" : "finished genome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-10-23T01:04:43Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "i_motif"
+      "lbl" : "finished_genome"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000160",
+      "meta" : {
+        "definition" : {
+          "val" : "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.",
+          "xrefs" : [ "ISBN:0-1767-2380-8" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "lambda_clone"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000163",
       "meta" : {
@@ -630,54 +744,81 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "splice donor site",
+          "val" : "donor splice site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "five prime splice site",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splice donor site",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "donor",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "five_prime_cis_splice_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001494",
+      "meta" : {
+        "definition" : {
+          "val" : "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length.",
+          "xrefs" : [ "PMID:11222754" ]
+        },
+        "comments" : [ "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "CDEII",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "donor splice site",
+          "val" : "centromere DNA Element II",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-11-09T05:51:26Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_cis_splice_site"
+      "lbl" : "centromere_DNA_Element_II"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000162",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001010",
       "meta" : {
         "definition" : {
-          "val" : "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.",
-          "xrefs" : [ "SO:cjm", "SO:ke" ]
+          "val" : "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH.",
+          "xrefs" : [ "PMID:9753739" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Splice_site"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice site",
+          "val" : "i motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "short intercalated motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "With spliceosomal introns, the splice sites bind the spliceosomal machinery."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_site"
+      "lbl" : "i_motif"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001493",
       "meta" : {
@@ -685,6 +826,7 @@
           "val" : "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p).",
           "xrefs" : [ "PMID:11222754" ]
         },
+        "comments" : [ "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Centromere DNA Element I",
@@ -697,9 +839,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-11-09T05:47:23Z"
@@ -710,6 +849,30 @@
       },
       "type" : "CLASS",
       "lbl" : "centromere_DNA_Element_I"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000162",
+      "meta" : {
+        "definition" : {
+          "val" : "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction.",
+          "xrefs" : [ "SO:cjm", "SO:ke" ]
+        },
+        "comments" : [ "With spliceosomal introns, the splice sites bind the spliceosomal machinery." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Splice_site"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "splice site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "splice_site"
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#position_of",
       "meta" : {
@@ -754,11 +917,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DNA constraint",
+          "val" : "DNA constraint sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DNA constraint sequence",
+          "val" : "DNA constraint",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -785,9 +948,43 @@
       },
       "type" : "CLASS",
       "lbl" : "tetraloop"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002339",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that encodes for a scaRNA (small Cajal body-specific RNA).",
+          "xrefs" : [ "PMID:27775477", "PMID:28869095" ]
+        },
+        "comments" : [ "Added as a request from FlyBase. See GitHub Issue #510" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Small Cajal body-specific RNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "scaRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-04-24T16:59:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "scaRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005849",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is a member of a group of genes that are either regulated or transcribed together within a larger group of genes that are regulated or transcribed together.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "gene subarray member",
@@ -803,6 +1000,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005848",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is a member of a gene cassette, which is a mobile genetic element.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "gene cassette member",
@@ -816,33 +1017,67 @@
       "type" : "CLASS",
       "lbl" : "gene_cassette_member"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001489",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002337",
       "meta" : {
         "definition" : {
-          "val" : "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.",
-          "xrefs" : [ "DOI:10.1126" ]
+          "val" : "Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules.",
+          "xrefs" : [ "PMID: 118436", "PMID: 29474379", "PMID: 3136294", "PMID:10788608", "PMID:407103", "PMID:4847940", "PMID:768488" ]
         },
+        "comments" : [ "Added as a request from FlyBase. See GitHub Issue #507. Renamed from rRNA_2S to cytosolic_2S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "annotation directed improvement",
+          "val" : "cytosolic rRNA 2S",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 2S rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-10-23T12:57:10Z"
+          "val" : "2021-04-23T22:59:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "annotation_directed_improved_draft"
+      "lbl" : "cytosolic_2S_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005847",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001489",
+      "meta" : {
+        "definition" : {
+          "val" : "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred.",
+          "xrefs" : [ "DOI:10.1126" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "annotation directed improvement",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-10-23T12:57:10Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "annotation_directed_improved_draft"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0005847",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is a member of a gene cassette, which is a mobile genetic element.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "cassette array member",
@@ -855,6 +1090,25 @@
       },
       "type" : "CLASS",
       "lbl" : "cassette_array_member"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001005",
+      "meta" : {
+        "definition" : {
+          "val" : "A region where the DNA does not contain an equal distrubution of all four possible nucleotides or does not contain all four nucleotides.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "low complexity region",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "low_complexity_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000158",
       "meta" : {
@@ -862,6 +1116,7 @@
           "val" : "A cloning vector that utilizes the E. coli F factor.",
           "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Fosmid"
         } ],
@@ -871,9 +1126,6 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -881,20 +1133,43 @@
       "type" : "CLASS",
       "lbl" : "fosmid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001005",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002338",
       "meta" : {
+        "definition" : {
+          "val" : "A 57 to 71 nucleotide RNA that is a component of the U7 small nuclear ribonucleoprotein complex (U7 snRNP). The U7 snRNP is required for histone pre-mRNA processing.",
+          "xrefs" : [ "PMID:15526162" ]
+        },
+        "comments" : [ "Added as a request from FlyBase. See GitHub Issue #508" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "low complexity region",
+          "val" : "U7 snRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small nuclear RNA U7",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U7 small nuclear RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snRNA U7",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-04-24T16:59:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "low_complexity_region"
+      "lbl" : "U7_snRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000157",
       "meta" : {
@@ -930,14 +1205,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-10-23T12:54:35Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -945,6 +1220,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001004",
       "meta" : {
+        "definition" : {
+          "val" : "When a sequence does not contain an equal distribution of all four possible nucleotide bases or does not contain all nucleotide bases.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "low complexity",
@@ -957,6 +1236,59 @@
       },
       "type" : "CLASS",
       "lbl" : "low_complexity"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0005845",
+      "meta" : {
+        "definition" : {
+          "val" : "An exon that is the only exon in a gene.",
+          "xrefs" : [ "RSC:cb" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "exon of single exon gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "single_exon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "singleton exon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "exon_of_single_exon_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002335",
+      "meta" : {
+        "definition" : {
+          "val" : "A stop codon with the DNA sequence TGA.",
+          "xrefs" : [ "https://en.wikipedia.org/wiki/Stop_codon" ]
+        },
+        "comments" : [ "Added as per GitHub request #537." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Opal stop codon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-04-21T21:16:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "opal_stop_codon"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001007",
       "meta" : {
@@ -964,6 +1296,7 @@
           "val" : "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes.",
           "xrefs" : [ "GOC:jl" ]
         },
+        "comments" : [ "This is not cryptic in the same sense as a cryptic gene or cryptic splice site." ],
         "xrefs" : [ {
           "val" : "http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w"
         } ],
@@ -973,9 +1306,6 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is not cryptic in the same sense as a cryptic gene or cryptic splice site."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -983,32 +1313,52 @@
       "type" : "CLASS",
       "lbl" : "cryptic_prophage"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005845",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001006",
       "meta" : {
         "definition" : {
-          "val" : "An exon that is the only exon in a gene.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\".",
+          "xrefs" : [ "GOC:jl" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Prophage"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "prophage"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002336",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera.",
+          "xrefs" : [ "PMID: 118436", "PMID: 29474379", "PMID: 3136294", "PMID:10788608", "PMID:407103", "PMID:4847940", "PMID:768488" ]
         },
+        "comments" : [ "Added as a request from FlyBase. See GitHub Issue #507. Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "single_exon",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "exon of single exon gene",
+          "val" : "2S rRNA gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "singleton exon",
+          "val" : "rRNA 2S gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-04-23T22:59:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exon_of_single_exon_gene"
+      "lbl" : "cytosolic_rRNA_2S_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000159",
       "meta" : {
@@ -1024,11 +1374,11 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nucleotide_deletion",
+          "val" : "nucleotide deletion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nucleotide deletion",
+          "val" : "nucleotide_deletion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -1045,23 +1395,6 @@
       },
       "type" : "CLASS",
       "lbl" : "deletion"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001006",
-      "meta" : {
-        "definition" : {
-          "val" : "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\".",
-          "xrefs" : [ "GOC:jl" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Prophage"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "prophage"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001485",
       "meta" : {
@@ -1069,13 +1402,14 @@
           "val" : "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies.",
           "xrefs" : [ "http:http://www.yeastgenome.org/help/glossary.html" ]
         },
+        "comments" : [ "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Y' element",
+          "val" : "Y prime element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:Y_prime_element",
+          "val" : "Y' element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasBroadSynonym",
@@ -1083,15 +1417,12 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Y prime element",
+          "val" : "INSDC_qualifier:Y_prime_element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-11-10T12:08:57Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -1102,58 +1433,30 @@
       },
       "type" : "CLASS",
       "lbl" : "Y_prime_element"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000154",
-      "meta" : {
-        "definition" : {
-          "val" : "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "P1 artificial chromosome",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "P1",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "PAC"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001001",
       "meta" : {
         "definition" : {
-          "val" : "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome.",
+          "val" : "Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Renamed from rRNA_23S to cytosolic_23S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "23S LSU rRNA",
+          "val" : "cytosolic rRNA 23S",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA 23S",
+          "val" : "cytosolic 23S LSU rRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "23S ribosomal RNA",
+          "val" : "cytosolic 23S ribosomal RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "23S rRNA",
+          "val" : "cytosolic 23S rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -1162,7 +1465,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_23S"
+      "lbl" : "cytosolic_23S_rRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005843",
       "meta" : {
@@ -1183,67 +1486,85 @@
       "type" : "CLASS",
       "lbl" : "rRNA_cleavage_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001484",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002333",
       "meta" : {
         "definition" : {
-          "val" : "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.",
-          "xrefs" : [ "http://www.yeastgenome.org/help/glossary.html" ]
+          "val" : "A stop codon with the DNA sequence TAG.",
+          "xrefs" : [ "https://en.wikipedia.org/wiki/Stop_codon" ]
         },
+        "comments" : [ "Added as per GitHub request #537." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:x_element_combinatorial_repeat",
+          "val" : "Amber stop codon",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-04-21T21:16:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "amber_stop_codon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000154",
+      "meta" : {
+        "definition" : {
+          "val" : "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome" ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "X element combinatorial repeat",
+          "val" : "P1 artificial chromosome",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "pred" : "hasExactSynonym",
+          "val" : "P1",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-11-10T11:03:37Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "X_element_combinatorial_repeat"
+      "lbl" : "PAC"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001000",
       "meta" : {
         "definition" : {
-          "val" : "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome.",
+          "val" : "Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Renamed to cytosolic_16S_rRNA from rRNA_16S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/16S_ribosomal_RNA"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "16S SSU RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "cytosolic 16S rRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "16S ribosomal RNA",
+          "val" : "cytosolic rRNA 16S",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "16S rRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 16S SSU RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA 16S",
+          "val" : "cytosolic 16S ribosomal RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -1252,7 +1573,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_16S"
+      "lbl" : "cytosolic_16S_rRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000153",
       "meta" : {
@@ -1260,15 +1581,13 @@
           "val" : "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host.",
           "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "bacterial artificial chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -1276,77 +1595,90 @@
       "type" : "CLASS",
       "lbl" : "BAC"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000156",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001484",
       "meta" : {
         "definition" : {
-          "val" : "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element.",
+          "xrefs" : [ "http://www.yeastgenome.org/help/glossary.html" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Cosmid"
-        } ],
+        "comments" : [ "X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cosmid vector",
+          "val" : "INSDC_qualifier:x_element_combinatorial_repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "X element combinatorial repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-11-10T11:03:37Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cosmid"
+      "lbl" : "X_element_combinatorial_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001487",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002334",
       "meta" : {
         "definition" : {
-          "val" : "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.",
-          "xrefs" : [ "DOI:10.1126" ]
+          "val" : "A stop codon with the DNA sequence TAA.",
+          "xrefs" : [ "https://en.wikipedia.org/wiki/Stop_codon" ]
         },
+        "comments" : [ "Added as per GitHub request #537." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "high quality draft",
+          "val" : "Ochre stop codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-10-23T12:52:36Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-04-21T21:16:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "high_quality_draft"
+      "lbl" : "ochre_stop_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001003",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001487",
       "meta" : {
         "definition" : {
-          "val" : "A recombination product between the 2 LTR of the same element.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome.",
+          "xrefs" : [ "DOI:10.1126" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "solo LTR",
+          "val" : "high quality draft",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Hadi Quesneville January 2007."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-10-23T12:52:36Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "solo_LTR"
+      "lbl" : "high_quality_draft"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005841",
       "meta" : {
@@ -1354,6 +1686,7 @@
           "val" : "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.",
           "xrefs" : [ "GOC:mah", "PMID:12457565" ]
         },
+        "comments" : [ "Has RNA 2'-O-ribose methylation guide activity (GO:0030561)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "methylation guide snoRNA",
@@ -1362,36 +1695,90 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Has RNA 2'-O-ribose methylation guide activity (GO:0030561)."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "methylation_guide_snoRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001002",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002331",
       "meta" : {
         "definition" : {
-          "val" : "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A region of DNA that is depleted of nucleosomes and accessible to DNA-binding proteins including transcription factors and nucleases.",
+          "xrefs" : [ "PMID:25903461", "SO:ds" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Added as part of GREEKC terms. See GitHub Issues #531 & #534." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA 25S",
+          "val" : "accessible DNA region",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-02-11T16:41:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "accessible_DNA_region"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000156",
+      "meta" : {
+        "definition" : {
+          "val" : "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Cosmid"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "25S ribosomal RNA",
+          "val" : "cosmid vector",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cosmid"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001003",
+      "meta" : {
+        "definition" : {
+          "val" : "A recombination product between the 2 LTR of the same element.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Requested by Hadi Quesneville January 2007." ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "25S LSU rRNA",
+          "val" : "solo LTR",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "solo_LTR"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000155",
+      "meta" : {
+        "definition" : {
+          "val" : "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "25S rRNA",
+          "val" : "plasmid sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -1400,7 +1787,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_25S"
+      "lbl" : "plasmid"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001486",
       "meta" : {
@@ -1414,55 +1801,80 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-10-23T12:48:32Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-10-23T12:48:32Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "standard_draft"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000155",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002332",
       "meta" : {
         "definition" : {
-          "val" : "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.",
+          "xrefs" : [ "SO:ds", "http://en.wikipedia.org/wiki/Epigenetics" ]
         },
+        "comments" : [ "Added as part of GREEKC terms to differentiate between inherited and not inherited epigenetic changes. See GitHub Issue #532." ],
+        "xrefs" : [ {
+          "val" : "https://epi.grants.cancer.gov/epigen/#:~:text=mail.nih.gov-,Overview,a%20cell%20or%20entire%20organism."
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plasmid sequence",
+          "val" : "epigenomically modified region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-02-11T21:16:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plasmid"
+      "lbl" : "epigenomically_modified_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000150",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001002",
       "meta" : {
         "definition" : {
-          "val" : "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.",
-          "xrefs" : [ "SO:rd" ]
+          "val" : "Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes.",
+          "xrefs" : [ "PMID:15493135", "PMID:2100998", "RSC:cb" ]
         },
+        "comments" : [ "Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 25S LSU rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic rRNA 25S",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 25S rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 25S ribosomal RNA",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "read"
+      "lbl" : "cytosolic_25S_rRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001481",
       "meta" : {
@@ -1478,63 +1890,90 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-09-09T05:26:10Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "RAPD"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001480",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000150",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence from the end of a PAC clone that may provide a highly specific marker.",
-          "xrefs" : [ "ZFIN:mh" ]
+          "val" : "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine.",
+          "xrefs" : [ "SO:rd" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "read"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002330",
+      "meta" : {
+        "definition" : {
+          "val" : "The region of mRNA 2 bases long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
+          "xrefs" : [ "SO:ds" ]
         },
+        "comments" : [ "Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "PAC end",
+          "val" : "minus 2 ribosomal frameshift",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "minus 2 translational frameshift",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "minus 2 ribosomal slippage",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-09-09T05:18:12Z"
+          "val" : "2021-02-03T20:33:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "PAC_end"
+      "lbl" : "minus_2_translational_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000152",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001480",
       "meta" : {
         "definition" : {
-          "val" : "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A region of sequence from the end of a PAC clone that may provide a highly specific marker.",
+          "xrefs" : [ "ZFIN:mh" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "yeast artificial chromosome",
+          "val" : "PAC end",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-09-09T05:18:12Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "YAC"
+      "lbl" : "PAC_end"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001483",
       "meta" : {
@@ -1562,26 +2001,25 @@
       "type" : "CLASS",
       "lbl" : "SNV"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001482",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000152",
       "meta" : {
+        "definition" : {
+          "val" : "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "shadow enhancer",
+          "val" : "yeast artificial chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-09-09T05:29:29Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "shadow_enhancer"
+      "lbl" : "YAC"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000151",
       "meta" : {
@@ -1601,84 +2039,130 @@
       "type" : "CLASS",
       "lbl" : "clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005837",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001482",
       "meta" : {
         "definition" : {
-          "val" : "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.",
-          "xrefs" : [ "PMID:2251119" ]
+          "val" : "An enhancer that drives the pattern of transcription and binds to the same TF as the primary enhancer, but is located in the intron of or on the far side of a neighboring gene.",
+          "xrefs" : [ "PMID:22083793" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U14 snoRNA primary transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "4.5S snRNA primary transcript",
+          "val" : "shadow enhancer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-09-09T05:29:29Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U14_snoRNA_primary_transcript"
+      "lbl" : "shadow_enhancer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001478",
+      "id" : "http://purl.obolibrary.org/obo/SO_0005839",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000403"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002328",
       "meta" : {
         "definition" : {
-          "val" : "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.",
-          "xrefs" : [ "ZFIN:dh" ]
+          "val" : "A splice_acceptor_variant (SO:0001574) that allows the transcript to escape nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
         },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "promoter trap construct",
+          "val" : "splice acceptor variant-NMD escaping",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splice acceptor variant-nonsense-mediated decay escaping",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-09-01T03:52:01Z"
+          "val" : "2020-12-30T17:12:30Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "promoter_trap_construct"
+      "lbl" : "splice_acceptor_variant_NMD_escaping"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005836",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002329",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence that is involved in the control of a biological process.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The region of mRNA 1 base long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
+          "xrefs" : [ "SO:ds" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Regulatory_region"
-        } ],
+        "comments" : [ "Added along with the update to the definition of transaltional_frameshift SO:0001210 Feb 2021, brought to our attention by Terrence Murphy of INSDC. See GitHub Issue #522." ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "pred" : "hasExactSynonym",
+          "val" : "minus 1 translational frameshift",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:other",
+          "val" : "minus 1 ribosomal slippage",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "regulatory region",
+          "val" : "minus 1 ribosomal frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-02-03T20:33:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regulatory_region"
+      "lbl" : "minus_1_translational_frameshift"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0005837",
+      "meta" : {
+        "definition" : {
+          "val" : "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.",
+          "xrefs" : [ "PMID:2251119" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "U14 snoRNA primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "4.5S snRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "U14_snoRNA_primary_transcript"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000147",
       "meta" : {
@@ -1686,6 +2170,7 @@
           "val" : "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Exon"
@@ -1698,13 +2183,110 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "exon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002326",
+      "meta" : {
+        "definition" : {
+          "val" : "A splice_donor_variant (SO:0001575) that allows the transcript to escape nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "splice donor variant-NMD escaping",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splice donor variant-nonsense-mediated decay escaping",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "splice_donor_variant_NMD_escaping"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0005836",
+      "meta" : {
+        "definition" : {
+          "val" : "A region of sequence that is involved in the control of a biological process.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Regulatory_region"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:other",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "regulatory region",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "regulatory_region"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001478",
+      "meta" : {
+        "definition" : {
+          "val" : "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic.",
+          "xrefs" : [ "ZFIN:dh" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "promoter trap construct",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-09-01T03:52:01Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "promoter_trap_construct"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000146",
+      "meta" : {
+        "definition" : {
+          "val" : "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "capped"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001477",
       "meta" : {
@@ -1731,19 +2313,65 @@
       "type" : "CLASS",
       "lbl" : "gene_trap_construct"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000146",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002327",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
         },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "splice acceptor variant-NMD triggering",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splice acceptor variant-nonsense-mediated decay triggering",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "capped"
+      "lbl" : "splice_acceptor_variant_NMD_triggering"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002324",
+      "meta" : {
+        "definition" : {
+          "val" : "A frameshift_variant (SO:0001589) that allows the transcript to escape nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "frameshift variant-nonsense-mediated decay escaping",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "frameshift variant-NMD escaping",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "frameshift_variant_NMD_escaping"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000149",
       "meta" : {
@@ -1807,6 +2435,36 @@
       },
       "type" : "CLASS",
       "lbl" : "supercontig"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002325",
+      "meta" : {
+        "definition" : {
+          "val" : "A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "splice donor variant-NMD triggering",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splice donor variant-nonsense-mediated decay triggering",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "splice_donor_variant_NMD_triggering"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000187",
       "meta" : {
@@ -1816,15 +2474,34 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "repeat_family"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002366",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for plastid rRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:00:08Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "plastid_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001034",
       "meta" : {
@@ -1832,16 +2509,40 @@
           "val" : "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage.",
           "xrefs" : [ "PMID:17589500", "SO:ma" ]
         },
+        "comments" : [ "Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "miRtron"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002367",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for plastid LSU rRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "plastid large subunit rRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:00:49Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "plastid_LSU_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000186",
       "meta" : {
@@ -1851,11 +2552,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "LTR retrotransposon",
+          "val" : "long terminal repeat retrotransposon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "long terminal repeat retrotransposon",
+          "val" : "LTR retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -1868,15 +2569,17 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001033",
       "meta" : {
+        "definition" : {
+          "val" : "DNA belonging to the genome of a chloroplast, a photosynthetic plastid.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "This term is used by MO." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "chloroplast DNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is used by MO."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -1884,24 +2587,39 @@
       "type" : "CLASS",
       "lbl" : "chloroplast_DNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001036",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002364",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that codes for mitochondrial LSU rRNA.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513). Obsoleted term rRNA_21S_gene (SO:0002241) merged into this term on 12 Sept 2022, see GitHub Issue #513." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "arginyl tRNA",
+          "val" : "mitochondrial large subunit rRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "rRNA_21S_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "rRNA 21S gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T04:57:49Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "arginyl_tRNA"
+      "lbl" : "mt_LSU_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000189",
       "meta" : {
@@ -1921,6 +2639,25 @@
       },
       "type" : "CLASS",
       "lbl" : "non_LTR_retrotransposon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001036",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "arginyl tRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "arginyl_tRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001035",
       "meta" : {
@@ -1932,16 +2669,16 @@
           "val" : "http://en.wikipedia.org/wiki/PiRNA"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:piRNA",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "piwi-associated RNA",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:piRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -1951,13 +2688,40 @@
       },
       "type" : "CLASS",
       "lbl" : "piRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002365",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for mitochondrial SSU rRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "mitochondrial small subunit rRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T04:58:07Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "mt_SSU_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000188",
       "meta" : {
         "definition" : {
           "val" : "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Intron"
@@ -1968,9 +2732,6 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -1987,19 +2748,19 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non-transcribed sequence",
+          "val" : "non transcribed region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nontranscribed region",
+          "val" : "nontranscribed sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non transcribed region",
+          "val" : "nontranscribed region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nontranscribed sequence",
+          "val" : "non-transcribed sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -2009,6 +2770,32 @@
       },
       "type" : "CLASS",
       "lbl" : "non_transcribed_region"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002362",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for cytosolic SSU rRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic small subunit rRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T04:37:02Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cytosolic_SSU_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001030",
       "meta" : {
@@ -2023,6 +2810,32 @@
       },
       "type" : "CLASS",
       "lbl" : "forward"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002363",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for mitochondrial rRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "mitochondrial rRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T04:55:58Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "mt_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000182",
       "meta" : {
@@ -2063,7 +2876,7 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "precursor RNA",
+          "val" : "primary transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -2071,11 +2884,11 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "primary transcript",
+          "val" : "INSDC_feature:prim_transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:prim_transcript",
+          "val" : "precursor RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -2088,6 +2901,11 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001032",
       "meta" : {
+        "definition" : {
+          "val" : "DNA belonging to the genome of a mitochondria.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "This terms is used by MO." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Mitochondrial_DNA"
         } ],
@@ -2101,9 +2919,6 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This terms is used by MO."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -2111,19 +2926,26 @@
       "type" : "CLASS",
       "lbl" : "mitochondrial_DNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001031",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002360",
       "meta" : {
         "definition" : {
-          "val" : "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that codes for cytosolic rRNA.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T04:30:40Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reverse"
+      "lbl" : "cytosolic_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000184",
       "meta" : {
@@ -2131,6 +2953,7 @@
           "val" : "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs.",
           "xrefs" : [ "PMID:9428511" ]
         },
+        "comments" : [ "May have either GT-AG or AT-AG 5' and 3' boundaries." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "U2 intron",
@@ -2139,13 +2962,50 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "May have either GT-AG or AT-AG 5' and 3' boundaries."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "U2_intron"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002361",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for cytosolic LSU rRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic large subunit rRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T04:32:20Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cytosolic_LSU_rRNA_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001031",
+      "meta" : {
+        "definition" : {
+          "val" : "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "reverse"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000181",
       "meta" : {
@@ -2177,6 +3037,10 @@
           "val" : "http://en.wikipedia.org/wiki/Retrotransposon"
         } ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "class I",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "retrotransposon element",
           "xrefs" : [ ]
@@ -2184,10 +3048,6 @@
           "pred" : "hasExactSynonym",
           "val" : "class I transposon",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "class I",
-          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -2196,6 +3056,27 @@
       },
       "type" : "CLASS",
       "lbl" : "retrotransposon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002359",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that encodes a Y RNA.",
+          "xrefs" : [ "PMID:1698620", "PMID:6187471", "PMID:6816230", "PMID:7520568", "PMID:7539809", "PMID:8836182" ]
+        },
+        "comments" : [ "There are four genes from HGNC that are annotated this way. HGNC IDs: 10242, 10243, 10244, and 10248." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-11T23:52:21Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "Y_RNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001027",
       "meta" : {
@@ -2250,9 +3131,39 @@
       },
       "type" : "CLASS",
       "lbl" : "genome"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002357",
+      "meta" : {
+        "definition" : {
+          "val" : "A physically clustered group of two or more genes in a particular genome that together encode a biosynthetic pathway for the production of a specialized metabolite (including its chemical variants).",
+          "xrefs" : [ "PMID:26284661" ]
+        },
+        "comments" : [ "See GitHub Issue #558." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Metabolic gene cluster",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-10-07T18:20:34Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "biosynthetic_gene_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001029",
       "meta" : {
+        "definition" : {
+          "val" : "The attribute of whether the sequence is the same direction as a feature (forward) or the opposite direction as a feature (reverse).",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "direction attribute",
@@ -2266,50 +3177,40 @@
       "type" : "CLASS",
       "lbl" : "direction_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001028",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002358",
       "meta" : {
         "definition" : {
-          "val" : "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.",
-          "xrefs" : [ "SO:immuno_workshop" ]
+          "val" : "A gene that encodes a vault RNA.",
+          "xrefs" : [ "PMID:19298825", "PMID:19491402", "PMID:22058117", "PMID:22926522", "PMID:30773316", "PMID:9535882" ]
         },
+        "comments" : [ "As of 11 November 2021 the HNGC lists 4 genes as RNA, vault. These are HGNC IDs: 12654, 12655, 12656, 37054." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-11T23:25:13Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "diplotype"
+      "lbl" : "vault_RNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000176",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001028",
       "meta" : {
         "definition" : {
-          "val" : "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known.",
+          "xrefs" : [ "SO:immuno_workshop" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "minus 35 signal",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:minus_35_signal",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "-35 signal",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_35_signal"
+      "lbl" : "diplotype"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001023",
       "meta" : {
@@ -2333,42 +3234,28 @@
       "type" : "CLASS",
       "lbl" : "allele"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000175",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000176",
       "meta" : {
         "definition" : {
-          "val" : "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Pribnow_box"
-        } ],
+        "comments" : [ "Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "-10 signal",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "minus 10 signal",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:minus_10_signal",
+          "val" : "-35 signal",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Pribnow box",
+          "val" : "minus 35 signal",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Pribnow-Schaller box",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Pribnow Schaller box",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "val" : "INSDC_qualifier:minus_35_signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -2377,35 +3264,165 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_10_signal"
+      "lbl" : "minus_35_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001022",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002355",
       "meta" : {
         "definition" : {
-          "val" : "The point within a chromosome where an inversion begins or ends.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A gene encoding a hpRNA.",
+          "xrefs" : [ "PMID:18463630", "PMID:18719707", "PMID:25544562" ]
         },
+        "comments" : [ "See GitHub Issue #518." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inversion breakpoint",
+          "val" : "Hairpin RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-10-07T17:09:18Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inversion_breakpoint"
+      "lbl" : "hpRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000178",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002356",
       "meta" : {
         "definition" : {
-          "val" : "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "An RNA comprising an extended inverted repeat, the stem of which is typically much longer than that of miRNA precursors and can be up to 400 base pairs in length. hpRNAs are processed by Dicer-2 to generate endogenous short interfering RNAs (siRNAs).",
+          "xrefs" : [ "PMID:18463630", "PMID:18719707", "PMID:25544562" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
+        "comments" : [ "See GitHub Issue #518." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Hairpin RNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-10-07T17:35:56Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "hpRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000175",
+      "meta" : {
+        "definition" : {
+          "val" : "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
+        },
+        "comments" : [ "Changed from is_a SO:0000713 DNA_motif to is_a SO:0002312 core_prokaryotic_promoter_element in response to GREEKC Initiative Dave Sant Aug 2020. Changed from is_a SO:0002312 core_prokaryotic_promoter_element back to is_a SO:0000713 DNA_motif to be consistent with minus_12_signal and minus_24_signal on 12 July 2021." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Pribnow_box"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "-10 signal",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:minus_10_signal",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Pribnow box",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Pribnow-Schaller box",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "minus 10 signal",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Pribnow Schaller box",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "minus_10_signal"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001022",
+      "meta" : {
+        "definition" : {
+          "val" : "The point within a chromosome where an inversion begins or ends.",
+          "xrefs" : [ "SO:cb" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "inversion breakpoint",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "inversion_breakpoint"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002353",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene encoding a stem-bulge RNA.",
+          "xrefs" : [ "PMID:25908866", "PMID:30666901" ]
+        },
+        "comments" : [ "See GitHub Issue #516." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Stem-bulge RNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stem_bulge_RNA_gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-09-30T21:25:37Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "sbRNA_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000178",
+      "meta" : {
+        "definition" : {
+          "val" : "The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Definition updated with per Mejia-Almonte et.al Redefining fundamental concepts of transcription initiation in prokaryotes Aug 5 2020." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Operon"
         } ],
         "synonyms" : [ {
@@ -2416,9 +3433,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
         } ]
       },
       "type" : "CLASS",
@@ -2443,22 +3457,35 @@
       "type" : "CLASS",
       "lbl" : "polymorphic_sequence_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001024",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002354",
       "meta" : {
         "definition" : {
-          "val" : "A haplotype is one of a set of coexisting sequence variants of a haplotype block.",
-          "xrefs" : [ "SO:immuno_workshop" ]
+          "val" : "A small non-coding stem-loop RNA present in nematodes and insects, functionally and structurally related to vertebrate Y RNA.",
+          "xrefs" : [ "PMID:25908866", "PMID:30666901" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Haplotype"
+        "comments" : [ "See GitHub Issue #516." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Stem-bulge RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stem_bulge_RNA",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-09-30T21:29:19Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "haplotype"
+      "lbl" : "sbRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000177",
       "meta" : {
@@ -2479,12 +3506,50 @@
       },
       "type" : "CLASS",
       "lbl" : "cross_genome_match"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001024",
+      "meta" : {
+        "definition" : {
+          "val" : "A haplotype is one of a set of coexisting sequence variants of a haplotype block.",
+          "xrefs" : [ "SO:immuno_workshop" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Haplotype"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "haplotype"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002351",
+      "meta" : {
+        "definition" : {
+          "val" : "A fragile site found in the chromosomes of less than five percent of the human population.",
+          "xrefs" : [ "PMID:16236432", "PMID:17608616" ]
+        },
+        "comments" : [ "See GitHub Issue #301." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-09-30T19:34:13Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "rare_fragile_site"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000172",
       "meta" : {
         "definition" : {
           "val" : "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/CAAT_box"
@@ -2495,11 +3560,11 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "CAAT-box",
+          "val" : "INSDC_qualifier:CAAT_signal",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:CAAT_signal",
+          "val" : "CAAT-box",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -2524,21 +3589,22 @@
           "val" : "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA polymerase C promoter",
+          "val" : "RNApol III promoter",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "pol III promoter",
+          "val" : "polymerase III promoter",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "RNApol III promoter",
+          "val" : "RNA polymerase C promoter",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polymerase III promoter",
+          "val" : "pol III promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -2549,42 +3615,35 @@
       "type" : "CLASS",
       "lbl" : "RNApol_III_promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000174",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002352",
       "meta" : {
         "definition" : {
-          "val" : "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).",
-          "xrefs" : [ "PMID:16858867", "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A non-coding RNA typically derived from intronic sequence of the sense strand of a cognate host gene, that is not rapidly degraded. It may contain exonic sequences, 5′ caps, and/or polyA tails.",
+          "xrefs" : [ "PMID:27147469", "PMID:29397203", "PMID:30391089" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/TATA_box"
-        } ],
+        "comments" : [ "See GitHub Issue #515." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Goldstein-Hogness box",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "TATA box",
+          "val" : "stable_intronic_sequence_RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:TATA_box",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "val" : "Stable intronic sequence RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Binds TBP."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-09-30T21:07:18Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TATA_box"
+      "lbl" : "sisRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001021",
       "meta" : {
@@ -2593,13 +3652,13 @@
           "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "aberration_junction",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasBroadSynonym",
           "val" : "INSDC_feature:misc_recomb",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "aberration_junction",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "chromosome breakpoint",
@@ -2614,51 +3673,66 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001242"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001242"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "chromosome_breakpoint"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001020",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000174",
       "meta" : {
+        "definition" : {
+          "val" : "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T).",
+          "xrefs" : [ "PMID:16858867", "http://www.insdc.org/files/feature_table.html" ]
+        },
+        "comments" : [ "Binds TBP." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/TATA_box"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mutation affecting copy number",
+          "val" : "TATA box",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting copy number",
+          "val" : "INSDC_qualifier:TATA_box",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Goldstein-Hogness box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001563"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_copy_number"
+      "lbl" : "TATA_box"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000173",
       "meta" : {
         "definition" : {
           "val" : "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:GC_rich_promoter_region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "GC-rich region",
           "xrefs" : [ ]
@@ -2666,22 +3740,59 @@
           "pred" : "hasExactSynonym",
           "val" : "GC rich promoter region",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "GC_rich_promoter_region"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001020",
+      "meta" : {
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "mutation affecting copy number",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:GC_rich_promoter_region",
+          "val" : "sequence variant affecting copy number",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001563"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_variant_affecting_copy_number"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002350",
+      "meta" : {
+        "definition" : {
+          "val" : "A fragile site considered part of the normal chromosomal structure.",
+          "xrefs" : [ "PMID: 16236432", "PMID: 17608616" ]
+        },
+        "comments" : [ "See GitHub Issue #301." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-09-30T19:33:59Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "GC_rich_promoter_region"
+      "lbl" : "common_fragile_site"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000170",
       "meta" : {
@@ -2689,7 +3800,12 @@
           "val" : "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221." ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polymerase II promoter",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "RNA polymerase B promoter",
           "xrefs" : [ ]
@@ -2697,10 +3813,6 @@
           "pred" : "hasRelatedSynonym",
           "val" : "pol II promoter",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "polymerase II promoter",
-          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "RNApol II promoter",
@@ -2726,11 +3838,11 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "copy number polymorphism",
+          "val" : "copy number variation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "copy number variation",
+          "val" : "copy number polymorphism",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -2749,28 +3861,35 @@
       "type" : "CLASS",
       "lbl" : "copy_number_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001016",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002348",
       "meta" : {
         "definition" : {
-          "val" : "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes.",
+          "xrefs" : [ "PMID: 24572720", "PMID:3044395" ]
         },
+        "comments" : [ "Added as a request from EMBL. See GitHub Issue #493" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "internal guide sequence",
+          "val" : "plastid large subunit rRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IGS",
+          "val" : "plastid LSU rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-06-10T16:45:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "internal_guide_sequence"
+      "lbl" : "plastid_LSU_rRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000169",
       "meta" : {
@@ -2778,9 +3897,10 @@
           "val" : "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polymerase I promoter",
+          "val" : "pol I promoter",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -2788,7 +3908,7 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "pol I promoter",
+          "val" : "polymerase I promoter",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -2803,15 +3923,19 @@
       "type" : "CLASS",
       "lbl" : "RNApol_I_promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0005858",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001016",
       "meta" : {
         "definition" : {
-          "val" : "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.",
-          "xrefs" : [ "http://www.informatics.jax.org/silverbook/glossary.shtml" ]
+          "val" : "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity.",
+          "xrefs" : [ "SO:cb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "syntenic region",
+          "val" : "IGS",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "internal guide sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -2820,50 +3944,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "syntenic_region"
+      "lbl" : "internal_guide_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000168",
+      "id" : "http://purl.obolibrary.org/obo/SO_0005858",
       "meta" : {
         "definition" : {
-          "val" : "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species.",
+          "xrefs" : [ "http://www.informatics.jax.org/silverbook/glossary.shtml" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "syntenic region",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_cut_site"
+      "lbl" : "syntenic_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001015",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001499",
       "meta" : {
         "definition" : {
-          "val" : "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.",
-          "xrefs" : [ "PMID:11256617" ]
+          "val" : "The status of whole genome sequence.",
+          "xrefs" : [ "DOI:10.1126" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Wobble_base_pair"
-        } ],
+        "comments" : [ "This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "wobble pair",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "wobble base pair",
+          "val" : "whole genome sequence status",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-10-23T12:47:47Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "wobble_base_pair"
+      "lbl" : "whole_genome_sequence_status"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005857",
       "meta" : {
@@ -2892,33 +4018,67 @@
       "type" : "CLASS",
       "lbl" : "selenocysteinyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001499",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000168",
       "meta" : {
         "definition" : {
-          "val" : "The status of whole genome sequence.",
-          "xrefs" : [ "DOI:10.1126" ]
+          "val" : "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "whole genome sequence status",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "restriction_enzyme_cut_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002349",
+      "meta" : {
+        "definition" : {
+          "val" : "A heritable locus on a chromosome that is prone to DNA breakage.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "See GitHub Issue #301." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-09-30T19:29:24Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "fragile_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001015",
+      "meta" : {
+        "definition" : {
+          "val" : "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C.",
+          "xrefs" : [ "PMID:11256617" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Wobble_base_pair"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "wobble base pair",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-10-23T12:47:47Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms."
+          "pred" : "hasExactSynonym",
+          "val" : "wobble pair",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "whole_genome_sequence_status"
+      "lbl" : "wobble_base_pair"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005856",
       "meta" : {
@@ -2945,13 +4105,11 @@
           "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells.",
           "xrefs" : [ "SO:cb", "http://en.wikipedia.org/wiki/Epitope" ]
         },
+        "comments" : [ "Requested by Trish Whetzel." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Epitope"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Trish Whetzel."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -2959,32 +4117,61 @@
       "type" : "CLASS",
       "lbl" : "epitope"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001017",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002346",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Plastid rRNA is an RNA component of the small or large subunits of plastid (such as chloroplast) ribosomes.",
+          "xrefs" : [ "PMID: 24572720", "PMID:3044395" ]
         },
-        "xrefs" : [ {
-          "val" : "loinc:LA6700-4"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Silent_mutation"
+        "comments" : [ "Added as a request from EMBL. See GitHub Issue #493" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "plastid rRNA",
+          "xrefs" : [ ]
         } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-06-10T16:45:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "plastid_rRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002347",
+      "meta" : {
+        "definition" : {
+          "val" : "Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes.",
+          "xrefs" : [ "PMID: 24572720", "PMID:3044395" ]
+        },
+        "comments" : [ "Added as a request from EMBL. See GitHub Issue #493" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silent mutation",
+          "val" : "plastid SSU rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "plastid small subunit rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-06-10T16:45:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silent_mutation"
+      "lbl" : "plastid_SSU_rRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0005855",
       "meta" : {
@@ -3005,6 +4192,31 @@
       },
       "type" : "CLASS",
       "lbl" : "gene_group"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001017",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Silent_mutation"
+        }, {
+          "val" : "loinc:LA6700-4"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "silent mutation",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "silent_mutation"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001056",
       "meta" : {
@@ -3012,6 +4224,7 @@
           "val" : "A regulatory_region that modulates splicing.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -3032,22 +4245,23 @@
           "val" : "A regulatory_region that modulates the transcription of a gene or genes.",
           "xrefs" : [ "PMID:9679020", "SO:regcreative" ]
         },
+        "comments" : [ "Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "INSDC_qualifier:transcriptional_cis_regulatory_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "transcriptional cis regulatory region",
+          "val" : "transcription-control region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "transcription-control region",
+          "val" : "transcriptional cis regulatory region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -3064,6 +4278,7 @@
           "val" : "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter.",
           "xrefs" : [ "SO:regcreative" ]
         },
+        "comments" : [ "Obsoleted Jan 21, 2021 by Dave Sant. GREEKC consortium individuals pointed out that this did not fit with the other child terms of transcriptional_cis_regulatory_region (SO:0001055), which are currently promoter, CRM and promoter flanking region. No comments about when this term was created exist, no references are listed. GREEKC members assume that this was previously under enhansosome (SO:0001057), which was probably created along with this term but has since been obsoleted. This term can be resurrected as non-obsolete if we can find a reference publication and/or change the name to a term that is commonly used in the field." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "promoter targeting sequence",
@@ -3072,7 +4287,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "promoter_targeting_sequence"
@@ -3082,10 +4298,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "enhanceosome"
@@ -3095,10 +4309,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "nested_repeat"
@@ -3106,12 +4318,10 @@
       "id" : "http://purl.obolibrary.org/obo/SO_0001051",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "nested_region"
@@ -3138,12 +4348,10 @@
       "id" : "http://purl.obolibrary.org/obo/SO_0001053",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "nested_transposon"
@@ -3152,43 +4360,109 @@
       "type" : "PROPERTY",
       "lbl" : "has_synonym_type"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001050",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002380",
       "meta" : {
         "definition" : {
-          "val" : "A portion of a repeat, interrupted by the insertion of another element.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that codes for pseudouridylation_guide_snoRNA. A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.",
+          "xrefs" : [ "PMID:12457565" ]
         },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "repeat fragment",
+          "val" : "pseudouridylation guide snoRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Chris Smith, and others at Flybase to help annotate nested repeats."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:51:40Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "repeat_fragment"
+      "lbl" : "pseudouridylation_guide_snoRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001049",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002381",
       "meta" : {
         "definition" : {
-          "val" : "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.",
-          "xrefs" : [ "Phigo:ariane" ]
+          "val" : "A long non-coding RNA which is produced using the promoter of a protein-coding gene but with transcription occurring in the opposite direction.",
+          "xrefs" : [ "PMID:30175284", "PMID:34956340" ]
         },
+        "comments" : [ "Created new term \"bidirectional_promoter_lncRNA\" (SO:0002381). See GitHub Issue #579." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "defective conjugative transposon",
+          "val" : "bidirectional_promoter_long_non-coding_RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "bidirectional promoter lncRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "bidirectional promoter long non-coding RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "bidirectional_lncRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "bidirectional lncRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2022-10-28T19:05:35Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "bidirectional_promoter_lncRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001050",
+      "meta" : {
+        "definition" : {
+          "val" : "A portion of a repeat, interrupted by the insertion of another element.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Requested by Chris Smith, and others at Flybase to help annotate nested repeats." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "repeat fragment",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "repeat_fragment"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001049",
+      "meta" : {
+        "definition" : {
+          "val" : "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.",
+          "xrefs" : [ "Phigo:ariane" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "defective conjugative transposon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
       },
       "type" : "CLASS",
       "lbl" : "defective_conjugative_transposon"
@@ -3199,6 +4473,7 @@
           "val" : "A region located within an inversion site.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A term created to allow the parts of an inversion site have an is_a path back to the root." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "inversion site part",
@@ -3207,13 +4482,62 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A term created to allow the parts of an inversion site have an is_a path back to the root."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "inversion_site_part"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002379",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for methylation_guide_snoRNA. A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue.",
+          "xrefs" : [ "PMID:12457565" ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "methylation guide snoRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:51:12Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "methylation_guide_snoRNA_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002377",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for U14_snoRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "small nucleolar RNA U14 gene, snoRNA U14 gene, U14 small nucleolar RNA gene, U14 snoRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:50:43Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "U14_snoRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000198",
       "meta" : {
@@ -3243,11 +4567,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cointegrated plasmid",
+          "val" : "cointegrated replicon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "cointegrated replicon",
+          "val" : "cointegrated plasmid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -3257,6 +4581,52 @@
       },
       "type" : "CLASS",
       "lbl" : "cointegrated_plasmid"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000197",
+      "meta" : {
+        "definition" : {
+          "val" : "The sequence of the three_prime_coding_exon that codes for protein.",
+          "xrefs" : [ "SO:cjm" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "three prime exon coding region",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "three_prime_coding_exon_coding_region"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002378",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for U3_snoRNA. U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "small nucleolar RNA U3 gene, snoRNA U3 gene, U3 small nucleolar RNA gene, U3 snoRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:50:57Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "U3_snoRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001044",
       "meta" : {
@@ -3264,6 +4634,7 @@
           "val" : "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence.",
           "xrefs" : [ "SO:xp" ]
         },
+        "comments" : [ "Definition change requested by Val, 3172757." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Numt"
         } ],
@@ -3281,9 +4652,6 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Definition change requested by Val, 3172757."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -3291,25 +4659,31 @@
       "type" : "CLASS",
       "lbl" : "nuclear_mt_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000197",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002375",
       "meta" : {
         "definition" : {
-          "val" : "The sequence of the three_prime_coding_exon that codes for protein.",
-          "xrefs" : [ "SO:cjm" ]
+          "val" : "A gene that codes a C_D_box_snoRNA. Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.",
+          "xrefs" : [ "PMID:12457565", "PMID:22065625" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime exon coding region",
+          "val" : "box C/D snoRNA gene, C D box snoRNA gene, C/D box snoRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:49:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_coding_exon_coding_region"
+      "lbl" : "C_D_box_snoRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001047",
       "meta" : {
@@ -3338,13 +4712,13 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "transchr",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "translocated sequence",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "transchr",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -3354,50 +4728,50 @@
       "type" : "CLASS",
       "lbl" : "translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001046",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002376",
       "meta" : {
         "definition" : {
-          "val" : "Component of the inversion site located at the left of a region susceptible to site-specific inversion.",
-          "xrefs" : [ "Phigo:at" ]
+          "val" : "A gene that codes for H_ACA_box_snoRNA. Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.",
+          "xrefs" : [ "PMID:12457565", "PMID:22065625" ]
         },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519). Added citations. See GitHub Issue #565." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "IRLinv site",
+          "val" : "box H/ACA snoRNA gene, H ACA box snoRNA gene, H/ACA box snoRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:50:14Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "IRLinv_site"
+      "lbl" : "H_ACA_box_snoRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001041",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001046",
       "meta" : {
         "definition" : {
-          "val" : "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Component of the inversion site located at the left of a region susceptible to site-specific inversion.",
+          "xrefs" : [ "Phigo:at" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "virus sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "viral sequence",
+          "val" : "IRLinv site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "viral_sequence"
+      "lbl" : "IRLinv_site"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000194",
       "meta" : {
@@ -3411,15 +4785,15 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "LINE element",
+          "val" : "LINE",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "LINE",
+          "val" : "Long interspersed nuclear element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Long interspersed nuclear element",
+          "val" : "LINE element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -3429,6 +4803,56 @@
       },
       "type" : "CLASS",
       "lbl" : "LINE_element"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001041",
+      "meta" : {
+        "definition" : {
+          "val" : "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "viral sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "virus sequence",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "viral_sequence"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002373",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs.",
+          "xrefs" : [ "PMID:17099227", "PMID:24659245" ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "H/ACA scaRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:40:58Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "H_ACA_box_scaRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000193",
       "meta" : {
@@ -3442,15 +4866,15 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "restriction fragment length polymorphism",
+          "val" : "RFLP",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "RFLP",
+          "val" : "RFLP fragment",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "RFLP fragment",
+          "val" : "restriction fragment length polymorphism",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -3461,34 +4885,41 @@
       "type" : "CLASS",
       "lbl" : "RFLP_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001040",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002374",
       "meta" : {
         "definition" : {
-          "val" : "A plasmid sequence that is integrated within the host chromosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that codes for scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs.",
+          "xrefs" : [ "PMID:17099227", "PMID:24659245" ]
         },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "integrated plasmid",
+          "val" : "C/D-H/ACA scaRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:41:06Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "integrated_plasmid"
+      "lbl" : "C-D_H_ACA_box_scaRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001043",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001040",
       "meta" : {
         "definition" : {
-          "val" : "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.",
-          "xrefs" : [ "Phigo:at" ]
+          "val" : "A plasmid sequence that is integrated within the host chromosome.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "attCtn site",
+          "val" : "integrated plasmid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -3497,7 +4928,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "attCtn_site"
+      "lbl" : "integrated_plasmid"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000196",
       "meta" : {
@@ -3519,16 +4950,15 @@
       "type" : "CLASS",
       "lbl" : "five_prime_coding_exon_coding_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000195",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001043",
       "meta" : {
         "definition" : {
-          "val" : "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.",
+          "xrefs" : [ "Phigo:at" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "coding exon",
+          "val" : "attCtn site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -3537,7 +4967,33 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_exon"
+      "lbl" : "attCtn_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002371",
+      "meta" : {
+        "definition" : {
+          "val" : "A scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs.",
+          "xrefs" : [ "PMID:17099227", "PMID:24659245" ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "C/D-H/ACA scaRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:35:23Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "C-D_H_ACA_box_scaRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001042",
       "meta" : {
@@ -3569,16 +5025,66 @@
       "type" : "CLASS",
       "lbl" : "phage_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000190",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002372",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs.",
+          "xrefs" : [ "PMID:17099227", "PMID:24659245" ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime intron",
+          "val" : "C/D scaRNA gene",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:40:46Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "C_D_box_scaRNA_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000195",
+      "meta" : {
+        "definition" : {
+          "val" : "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "coding exon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "coding_exon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000190",
+      "meta" : {
+        "definition" : {
+          "val" : "An intron that is the most 5-prime in a given transcript.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "5' intron sequence",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime intron",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "5' intron",
@@ -3591,10 +5097,44 @@
       },
       "type" : "CLASS",
       "lbl" : "five_prime_intron"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002370",
+      "meta" : {
+        "definition" : {
+          "val" : "A scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs.",
+          "xrefs" : [ "PMID:17099227", "PMID:24659245" ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "H/ACA scaRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:35:04Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "H_ACA_box_scaRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000192",
       "meta" : {
+        "definition" : {
+          "val" : "An intron that is the most 3-prime in a given transcript.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "3' intron sequence",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "3' intron",
           "xrefs" : [ ]
@@ -3602,10 +5142,6 @@
           "pred" : "hasExactSynonym",
           "val" : "three prime intron",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "3' intron sequence",
-          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -3617,6 +5153,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000191",
       "meta" : {
+        "definition" : {
+          "val" : "An intron that is not the most 3-prime or the most 5-prime in a given transcript.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "interior intron",
@@ -3661,15 +5201,15 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:mobile_element",
+          "val" : "MGE",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "MGE",
+          "val" : "mobile genetic element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "mobile genetic element",
+          "val" : "INSDC_feature:mobile_element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -3679,6 +5219,32 @@
       },
       "type" : "CLASS",
       "lbl" : "mobile_genetic_element"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002368",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that codes for plastid SSU rRNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "plastid small subunit rRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:01:03Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "plastid_SSU_rRNA_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001039",
       "meta" : {
@@ -3699,6 +5265,32 @@
       },
       "type" : "CLASS",
       "lbl" : "integrated_mobile_genetic_element"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002369",
+      "meta" : {
+        "definition" : {
+          "val" : "A scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs.",
+          "xrefs" : [ "PMID:17099227", "PMID:24659245" ]
+        },
+        "comments" : [ "Added at the request of Steven Marygold. See GitHub Issue #519 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/519)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "C/D scaRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2021-11-19T05:34:44Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "evan"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "C_D_box_scaRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#contains",
       "meta" : {
@@ -3706,12 +5298,10 @@
           "val" : "The inverse of contained_by.",
           "xrefs" : [ "PMID:20226267" ]
         },
+        "comments" : [ "Example: pre_miRNA contains miRNA_loop." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2010-10-14T01:32:15Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: pre_miRNA contains miRNA_loop."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -3729,30 +5319,35 @@
           "val" : "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Biosapien term was secondary_structure." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Secondary_structure"
         } ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide secondary structure",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "secondary structure",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "secondary_structure",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "2nary structure",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "polypeptide secondary structure",
-          "xrefs" : [ ]
+          "val" : "secondary structure region",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "secondary structure region",
-          "xrefs" : [ ]
+          "val" : "2nary structure",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
@@ -3760,9 +5355,6 @@
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Biosapien term was secondary_structure."
         } ]
       },
       "type" : "CLASS",
@@ -3777,16 +5369,18 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "transmembrane",
-          "xrefs" : [ ]
+          "val" : "transmem",
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "transmembrane polypeptide region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "transmem",
-          "xrefs" : [ "uniprot:feature_type" ]
+          "val" : "transmembrane",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -3816,7 +5410,8 @@
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "structural_motif",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -3835,29 +5430,29 @@
           "val" : "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm.",
           "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
         },
+        "comments" : [ "This could be inside an organelle within the cell." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "non cytoplasmic polypeptide region",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "non_cytoplasm_location",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "outside",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non cytoplasmic polypeptide region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00144"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This could be inside an organelle within the cell."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -3871,17 +5466,19 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "cytoplasm_location",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "cytoplasmic polypeptide region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "inside",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytoplasm_location",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
@@ -3904,7 +5501,8 @@
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "membrane_loop",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "membrane peptide loop",
@@ -3929,20 +5527,21 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "intramembrane",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "intramembrane polypeptide region",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "intramembrane",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00156"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -3954,25 +5553,23 @@
           "val" : "Region of polypeptide with a given structural property.",
           "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "structural_region",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "polypeptide structural region",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "structural_region",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00337"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00337"
         } ]
       },
       "type" : "CLASS",
@@ -3984,33 +5581,34 @@
           "val" : "Polypeptide region that is localized outside of a lipid bilayer.",
           "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "extramembrane polypeptide region",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "extramembrane_region",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "extramembrane",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "extramembrane_region",
+          "pred" : "hasExactSynonym",
+          "val" : "extramembrane polypeptide region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "topo_dom",
-          "xrefs" : [ "uniprot:feature_type" ]
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00154"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00154"
         } ]
       },
       "type" : "CLASS",
@@ -4022,6 +5620,7 @@
           "val" : "Arrangement of the polypeptide with respect to the lipid bilayer.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -4031,9 +5630,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00128"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -4048,20 +5644,18 @@
           "val" : "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.).",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "motif",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "polypeptide motif",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "motif",
+          "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00032"
         }, {
@@ -4078,18 +5672,15 @@
           "val" : "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length.",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "compositionally_biased_region",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "compositionally biased",
+          "val" : "compositional bias",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "compositional bias",
+          "pred" : "hasExactSynonym",
+          "val" : "compositionally_biased_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
@@ -4099,11 +5690,12 @@
           "pred" : "hasRelatedSynonym",
           "val" : "compositionally biased region of peptide",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "compositionally biased",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00068"
         }, {
@@ -4113,6 +5705,19 @@
       },
       "type" : "CLASS",
       "lbl" : "compositionally_biased_region_of_peptide"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001069",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000417"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001068",
       "meta" : {
@@ -4120,6 +5725,7 @@
           "val" : "A polypeptide_repeat is a single copy of an internal sequence repetition.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -4136,9 +5742,6 @@
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
         } ]
       },
       "type" : "CLASS",
@@ -4150,6 +5753,7 @@
           "val" : "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -4159,9 +5763,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00129"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -4176,6 +5777,7 @@
           "val" : "Part of a peptide chain which is cleaved off during the formation of the mature protein.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Propeptide"
@@ -4190,18 +5792,28 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00077"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "propeptide"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001065",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001149"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001064",
       "meta" : {
@@ -4209,6 +5821,7 @@
           "val" : "Active peptides are proteins which are biologically active, released from a precursor molecule.",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Peptide"
@@ -4223,14 +5836,11 @@
           "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00076"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -4242,6 +5852,7 @@
           "val" : "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Discrete." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -4249,14 +5860,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00063"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -4269,21 +5877,24 @@
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:sequence_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "ANNOVAR:unknown",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "VAAST:sequence_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:sequence_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -4299,30 +5910,27 @@
           "val" : "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Merged with partially characterized change in nucleotide sequence." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence variation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_feature",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:variation",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "partially_characterised_change_in_DNA_sequence",
+          "pred" : "hasRelatedSynonym",
+          "val" : "sequence variation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "INSDC_note:sequence_alteration",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "partially characterised change in DNA sequence",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_feature",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:variation",
+          "pred" : "hasNarrowSynonym",
+          "val" : "partially characterised change in DNA sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasNarrowSynonym",
@@ -4332,19 +5940,20 @@
           "pred" : "hasExactSynonym",
           "val" : "sequence alteration",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "partially_characterised_change_in_DNA_sequence",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000007"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000004"
+          "val" : "SO:1000007"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Merged with partially characterized change in nucleotide sequence."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000004"
         } ]
       },
       "type" : "CLASS",
@@ -4386,11 +5995,11 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Cu_contact_site",
+          "val" : "polypeptide copper ion contact site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide copper ion contact site",
+          "val" : "Cu_contact_site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -4413,11 +6022,11 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Co_contact_site",
+          "val" : "polypeptide cobalt ion contact site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide cobalt ion contact site",
+          "val" : "Co_contact_site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -4440,19 +6049,19 @@
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Mg_contact_site",
+          "val" : "polypeptide magnesium ion contact site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide magnesium ion contact site",
+          "val" : "Mg_contact_site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00187"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00187"
         } ]
       },
       "type" : "CLASS",
@@ -4475,11 +6084,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00137"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -4491,6 +6100,7 @@
           "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions.",
           "xrefs" : [ "EBIBS:GAR", "SO:cb", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Residue is part of a binding site for a metal ion." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
@@ -4498,9 +6108,6 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Residue is part of a binding site for a metal ion."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00027"
         }, {
@@ -4517,33 +6124,29 @@
           "val" : "Binding site for any chemical group (co-enzyme, prosthetic group, etc.).",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Discrete." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "non covalent binding site",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "binding",
-          "xrefs" : [ "uniprot:curation" ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "binding site",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "binding",
+          "xrefs" : [ "uniprot:curation" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00029"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00029"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "non_covalent_binding_site"
@@ -4554,23 +6157,25 @@
           "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Residue involved in contact with calcium." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide calcium ion contact site",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "ca bind",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide calcium ion contact site",
-          "xrefs" : [ ]
+          "val" : "ca_bind",
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "Ca_contact_site",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ca_bind",
-          "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -4578,9 +6183,6 @@
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00186"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Residue involved in contact with calcium."
         } ]
       },
       "type" : "CLASS",
@@ -4597,10 +6199,6 @@
           "val" : "http://en.wikipedia.org/wiki/Protein_protein_interaction"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "protein protein contact",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "protein protein contact site",
           "xrefs" : [ ]
@@ -4608,13 +6206,17 @@
           "pred" : "hasRelatedSynonym",
           "val" : "protein_protein_interaction",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "protein protein contact",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00131"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -4635,13 +6237,11 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00246"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "covalent_binding_site"
@@ -4652,15 +6252,13 @@
           "val" : "X is transcribed_from Y if X is synthesized from template Y.",
           "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
+        "comments" : [ "Example: primary_transcript transcribed_from gene." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-08-19T12:05:39Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: primary_transcript transcribed_from gene."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -4686,6 +6284,7 @@
           "val" : "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein.",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Discrete." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Post_translational_modification"
@@ -4694,21 +6293,18 @@
           "pred" : "hasExactSynonym",
           "val" : "modified residue",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "post_translational_modification",
-          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "mod_res",
           "xrefs" : [ "uniprot:feature_type" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "post_translational_modification",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00052"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -4723,27 +6319,28 @@
           "val" : "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules.",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "2 discreet & joined." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "disulphide",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "disulphide bond",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "disulfide bond",
+          "val" : "disulfid",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "disulfid",
+          "pred" : "hasExactSynonym",
+          "val" : "disulphide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "disulfide",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "disulfide bond",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
@@ -4751,13 +6348,8 @@
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "2 discreet & joined."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "disulfide_bond"
@@ -4768,6 +6360,7 @@
           "val" : "Different sources report differing sequences.",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Discrete." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -4775,14 +6368,11 @@
           "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00069"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -4794,15 +6384,16 @@
           "val" : "The residue at an extremity of the sequence is not the terminal residue.",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Discrete." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "non terminal",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "non_ter",
           "xrefs" : [ "uniprot:feature_type" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non terminal",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -4810,9 +6401,6 @@
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00072"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
         } ]
       },
       "type" : "CLASS",
@@ -4826,24 +6414,22 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "crosslink",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "cross link",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "crosslink",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00178"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "cross_link"
@@ -4856,13 +6442,13 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:unsure",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "unsure",
           "xrefs" : [ "uniprot:feature_type" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:unsure",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
@@ -4874,6 +6460,21 @@
       },
       "type" : "CLASS",
       "lbl" : "sequence_uncertainty"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#non_functional_homolog_of",
+      "meta" : {
+        "definition" : {
+          "val" : "A relationship between a pseudogenic feature and its functional ancestor.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "non_functional_homolog_of"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001081",
       "meta" : {
@@ -4886,13 +6487,14 @@
           "pred" : "hasExactSynonym",
           "val" : "helix-turn-helix",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "helix turn helix",
-          "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "HTH",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "helix turn helix",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -4905,21 +6507,6 @@
       },
       "type" : "CLASS",
       "lbl" : "helix_turn_helix"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#non_functional_homolog_of",
-      "meta" : {
-        "definition" : {
-          "val" : "A relationship between a pseudogenic feature and its functional ancestor.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "non_functional_homolog_of"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001080",
       "meta" : {
@@ -4927,23 +6514,22 @@
           "val" : "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope.",
           "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Coiled_coil"
         } ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "coiled",
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "coiled coil",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "coiled",
-          "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00041"
         }, {
@@ -4962,13 +6548,13 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "non_cons",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "non consecutive",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non_cons",
+          "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
@@ -4987,6 +6573,7 @@
           "val" : "Incompatibility in the sequence due to some experimental problem.",
           "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
@@ -4996,9 +6583,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "BS:00125"
@@ -5013,18 +6597,16 @@
           "val" : "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary.",
           "xrefs" : [ "PMID:20226267" ]
         },
+        "comments" : [ "Example: start_codon starts CDS." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2010-10-14T01:47:53Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: start_codon starts CDS."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "PROPERTY",
@@ -5033,15 +6615,6 @@
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
       "type" : "PROPERTY",
       "lbl" : "has_obo_namespace"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#biosapiens",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "biosapiens protein feature ontology"
-        } ]
-      },
-      "type" : "PROPERTY"
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#connects_on",
       "meta" : {
@@ -5049,18 +6622,16 @@
           "val" : "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z.",
           "xrefs" : [ "PMID:20226267" ]
         },
+        "comments" : [ "Example: A splice_junction connects_on exon, exon, mature_transcript." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: A splice_junction connects_on exon, exon, mature_transcript."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T01:38:51Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T01:38:51Z"
         } ]
       },
       "type" : "PROPERTY",
@@ -5068,10 +6639,8 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#has_quality",
       "meta" : {
+        "comments" : [ "The relationship between a feature and an attribute." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The relationship between a feature and an attribute."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -5085,12 +6654,10 @@
           "val" : "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222."
         } ]
       },
       "type" : "PROPERTY",
@@ -5105,7 +6672,8 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Jannovar:internal_feature_elongation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "internal feature elongation",
@@ -5141,17 +6709,18 @@
         }, {
           "pred" : "hasExactSynonym",
           "val" : "VEP:feature_elongation",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-12T05:05:56Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -5166,25 +6735,27 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Jannovar:frameshift_elongation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "ANNOVAR:frameshift insertion",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "frameshift elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-12T05:10:05Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -5196,6 +6767,7 @@
           "val" : "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA.",
           "xrefs" : [ "PMID:19638999" ]
         },
+        "comments" : [ "Relationship is_a SO:0000644 antisense_RNA added 23 April 2021. See GitHub Issue #443" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "natural antisense transcript",
@@ -5206,18 +6778,31 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-06T04:36:44Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-06T04:36:44Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "antisense_lncRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001903",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0002131"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001906",
       "meta" : {
@@ -5229,27 +6814,29 @@
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:feature_truncation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "feature truncation",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:feature_truncation",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "VEP:feature_truncation",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-12T05:05:28Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-12T05:05:28Z"
         } ]
       },
       "type" : "CLASS",
@@ -5263,11 +6850,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "centromere outer repeat transcript",
+          "val" : "regional centromere outer repeat region transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "regional centromere outer repeat region transcript",
+          "val" : "centromere outer repeat transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -5275,14 +6862,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-11T04:54:22Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -5290,28 +6877,16 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001900",
       "meta" : {
-        "definition" : {
-          "val" : "A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components.",
-          "xrefs" : [ "PMID:15448137" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "m26 site",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-06T12:02:10Z"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001843"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "M26_binding_site"
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001902",
       "meta" : {
@@ -5327,12 +6902,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-06T12:23:32Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -5350,14 +6925,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-06T12:05:24Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -5365,12 +6940,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#associated_with",
       "meta" : {
+        "comments" : [ "This relationship is vague and up for discussion." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This relationship is vague and up for discussion."
         } ]
       },
       "type" : "PROPERTY",
@@ -5392,14 +6965,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-17T12:28:53Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -5425,66 +6998,66 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-06-17T12:26:35Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-06-17T12:26:35Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "mitochondrial_targeting_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001805",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000958",
       "meta" : {
         "definition" : {
-          "val" : "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN.",
-          "xrefs" : [ "PMID:12208841", "PMID:1842691" ]
+          "val" : "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.",
+          "xrefs" : [ "SO:ma" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "D-box",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "destruction box",
+          "val" : "circular double stranded DNA chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-06-17T12:16:02Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "destruction_box"
+      "lbl" : "circular_double_stranded_DNA_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000958",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001805",
       "meta" : {
         "definition" : {
-          "val" : "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN.",
+          "xrefs" : [ "PMID:12208841", "PMID:1842691" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "circular double stranded DNA chromosome",
+          "val" : "destruction box",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "D-box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-06-17T12:16:02Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "circular_double_stranded_DNA_chromosome"
+      "lbl" : "destruction_box"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001804",
       "meta" : {
@@ -5492,6 +7065,7 @@
           "val" : "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases.",
           "xrefs" : [ "PMID:18794354", "PMID:19818632" ]
         },
+        "comments" : [ "Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "DDB-box",
@@ -5502,17 +7076,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-17T12:10:44Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -5551,64 +7122,77 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-06-17T12:24:14Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-06-17T12:24:14Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "KEN_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001806",
+      "id" : "http://purl.obolibrary.org/obo/BS_00178",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001087"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000959",
       "meta" : {
         "definition" : {
-          "val" : "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL.",
-          "xrefs" : [ "PMID:2077689", "doi:10.1093/jxb/50.331.157" ]
+          "val" : "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.",
+          "xrefs" : [ "SO:ma" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ER retention signal",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "endoplasmic reticulum retention signal",
+          "val" : "linear single stranded DNA chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-06-17T12:19:49Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ER_retention_signal"
+      "lbl" : "linear_single_stranded_DNA_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000959",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001806",
       "meta" : {
         "definition" : {
-          "val" : "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL.",
+          "xrefs" : [ "PMID:2077689", "doi:10.1093/jxb/50.331.157" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "linear single stranded DNA chromosome",
+          "val" : "endoplasmic reticulum retention signal",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ER retention signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-06-17T12:19:49Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "linear_single_stranded_DNA_chromosome"
+      "lbl" : "ER_retention_signal"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001801",
       "meta" : {
@@ -5624,12 +7208,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-05-31T03:27:35Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -5666,14 +7250,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-31T03:24:06Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-31T03:24:06Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -5723,6 +7307,7 @@
           "val" : "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Term requested by M. Dumontier, June 1 2011." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "decreased polyadenylation variant",
@@ -5737,9 +7322,6 @@
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term requested by M. Dumontier, June 1 2011."
         } ]
       },
       "type" : "CLASS",
@@ -5751,23 +7333,21 @@
           "val" : "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Term requested by M. Dumontier, June 1 2011." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "increased polyadenylation variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term requested by M. Dumontier, June 1 2011."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-01T10:53:12Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -5832,6 +7412,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000951",
       "meta" : {
+        "definition" : {
+          "val" : "A signal for RNA polymerase to terminate transcription.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "eukaryotic terminator",
@@ -5847,6 +7431,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001217",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is a member of a group of genes that are either regulated or transcribed together.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "member of regulon",
@@ -5859,6 +7447,71 @@
       },
       "type" : "CLASS",
       "lbl" : "member_of_regulon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00182",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001083"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00181",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001086"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00187",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001098"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00186",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001094"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00185",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001103"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000947",
       "meta" : {
@@ -5868,11 +7521,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "res site",
+          "val" : "resolution site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "resolution site",
+          "val" : "res site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -5931,6 +7584,7 @@
           "val" : "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites.",
           "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "inversion site",
@@ -5939,9 +7593,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase."
         } ]
       },
       "type" : "CLASS",
@@ -5992,13 +7643,13 @@
           "xrefs" : [ "SO:as" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "attPB'",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "attR site",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "attPB'",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -6016,11 +7667,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "attBP'",
+          "val" : "attL site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "attL site",
+          "val" : "attBP'",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -6052,6 +7703,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000940",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is recombinationally rearranged.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "recombinationally rearranged",
@@ -6084,15 +7739,15 @@
       "type" : "CLASS",
       "lbl" : "orphan_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001246",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000981",
       "meta" : {
         "definition" : {
-          "val" : "A CDS with the evidence status of being independently known.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A transcription terminator that is dependent upon Rho.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CDS independently known",
+          "val" : "rho dependent bacterial terminator",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -6101,13 +7756,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CDS_independently_known"
+      "lbl" : "rho_dependent_bacterial_terminator"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000981",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001246",
       "meta" : {
+        "definition" : {
+          "val" : "A CDS with the evidence status of being independently known.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rho dependent bacterial terminator",
+          "val" : "CDS independently known",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -6116,7 +7775,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rho_dependent_bacterial_terminator"
+      "lbl" : "CDS_independently_known"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000980",
       "meta" : {
@@ -6133,11 +7792,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0000974"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0000974"
         } ]
       },
       "type" : "CLASS",
@@ -6161,6 +7820,71 @@
       },
       "type" : "CLASS",
       "lbl" : "CDS_supported_by_domain_match_data"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00151",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001113"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00155",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001076"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00154",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001072"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00153",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001118"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00152",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001114"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001827",
       "meta" : {
@@ -6168,20 +7892,18 @@
           "val" : "A sequencer read of an mRNA substrate.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience June, 2011." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "mRNA read",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience June, 2011."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-28T04:04:32Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -6189,6 +7911,19 @@
       },
       "type" : "CLASS",
       "lbl" : "mRNA_read"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00159",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000418"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001826",
       "meta" : {
@@ -6202,29 +7937,31 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Jannovar:disruptive_inframe_deletion",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "disruptive decrease in CDS length",
-          "xrefs" : [ ]
+          "val" : "snpEff:CODON_CHANGE_PLUS_CODON_DELETION",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:CODON_CHANGE_PLUS_CODON_DELETION",
+          "val" : "disruptive inframe deletion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "disruptive inframe deletion",
+          "val" : "disruptive decrease in CDS length",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-27T11:31:31Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -6248,6 +7985,19 @@
       },
       "type" : "CLASS",
       "lbl" : "gRNA_encoding"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00158",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001077"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001829",
       "meta" : {
@@ -6255,27 +8005,38 @@
           "val" : "A contig composed of mRNA_reads.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience June, 2011." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "mRNA contig",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-28T04:07:09Z"
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-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience June, 2011."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "mRNA_contig"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00157",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001105"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001828",
       "meta" : {
@@ -6285,11 +8046,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "genomic DNA read",
+          "val" : "gDNA_read",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "gDNA_read",
+          "val" : "genomic DNA read",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -6299,35 +8060,29 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
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-          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "genomic_DNA_read"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001251",
+      "id" : "http://purl.obolibrary.org/obo/BS_00156",
       "meta" : {
-        "definition" : {
-          "val" : "A CDS that is supported by sequence similarity data.",
-          "xrefs" : [ "SO:xp" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "CDS supported by sequence similarity data",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001075"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "CDS_supported_by_sequence_similarity_data"
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001823",
       "meta" : {
@@ -6337,26 +8092,45 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "conservative increase in CDS length",
+          "val" : "conservative inframe insertion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conservative inframe insertion",
+          "val" : "conservative increase in CDS length",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-27T11:28:02Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "conservative_inframe_insertion"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1001251",
+      "meta" : {
+        "definition" : {
+          "val" : "A CDS that is supported by sequence similarity data.",
+          "xrefs" : [ "SO:xp" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "CDS supported by sequence similarity data",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "CDS_supported_by_sequence_similarity_data"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000976",
       "meta" : {
@@ -6371,6 +8145,25 @@
       },
       "type" : "CLASS",
       "lbl" : "cryptic"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000975",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene found within a minicircle.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "minicircle gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "minicircle_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001822",
       "meta" : {
@@ -6379,80 +8172,70 @@
           "xrefs" : [ "EBI:gr" ]
         },
         "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         }, {
           "val" : "http://vat.gersteinlab.org/formats.php"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inframe decrease in CDS length",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "inframe_codon_loss",
-          "xrefs" : [ ]
+          "val" : "VEP:inframe_deletion",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:inframe_deletion",
-          "xrefs" : [ ]
+          "val" : "ANNOVAR:nonframeshift deletion",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAT:deletionNFS",
+          "val" : "inframe_codon_loss",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "inframe codon loss",
+          "val" : "snpEff:CODON_DELETION",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "inframe decrease in CDS length",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "inframe deletion",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAT:deletionNFS",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "snpEff:CODON_DELETION",
+          "val" : "inframe codon loss",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:nonframeshift deletion",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "Jannovar:inframe_deletion",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "SO:0001652"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-27T11:27:10Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "inframe_deletion"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000975",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "minicircle gene",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "minicircle_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001825",
       "meta" : {
@@ -6461,23 +8244,23 @@
           "xrefs" : [ "EBI:gr" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "conservative decrease in CDS length",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "conservative inframe deletion",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "conservative decrease in CDS length",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-27T11:30:43Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -6491,11 +8274,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "information region",
+          "val" : "template region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "template region",
+          "val" : "information region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -6508,15 +8291,13 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000977",
       "meta" : {
+        "comments" : [ "Part of an edited transcript only." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "anchor binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Part of an edited transcript only."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -6540,84 +8321,59 @@
         }, {
           "pred" : "hasExactSynonym",
           "val" : "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:disruptive_inframe_insertion",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "disruptive increase in CDS length",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:disruptive_inframe_insertion",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-27T11:28:37Z"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "disruptive_inframe_insertion"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000972",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "RNA replication mode",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This has been obsoleted as it represents a process. replaced_by: GO:0034961."
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_replication_mode"
+      "lbl" : "disruptive_inframe_insertion"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001255",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "status_of_coding_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000971",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000972",
       "meta" : {
+        "comments" : [ "This has been obsoleted as it represents a process. replaced_by: GO:0034961." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DNA replication mode",
+          "val" : "RNA replication mode",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This has been obsoleted as it represents a process. replaced_by: GO:0006260."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "DNA_replication_mode"
+      "lbl" : "RNA_replication_mode"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001254",
       "meta" : {
@@ -6637,6 +8393,23 @@
       },
       "type" : "CLASS",
       "lbl" : "CDS_predicted"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000971",
+      "meta" : {
+        "comments" : [ "This has been obsoleted as it represents a process. replaced_by: GO:0006260." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "DNA replication mode",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "DNA_replication_mode"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001821",
       "meta" : {
@@ -6645,55 +8418,60 @@
           "xrefs" : [ "EBI:gr" ]
         },
         "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
           "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
         }, {
           "val" : "http://vat.gersteinlab.org/formats.php"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "inframe increase in CDS length",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "Jannovar:inframe_insertion",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "inframe_codon_gain",
-          "xrefs" : [ ]
+          "val" : "snpEFF:CODON_INSERTION",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "inframe insertion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEFF:CODON_INSERTION",
-          "xrefs" : [ ]
+          "val" : "VAT:insertionNFS",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:nonframeshift insertion",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
+          "val" : "VEP:inframe_insertion",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:inframe_insertion",
-          "xrefs" : [ ]
+          "val" : "ANNOVAR:nonframeshift insertion",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAT:insertionNFS",
+          "val" : "inframe increase in CDS length",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "inframe codon gain",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "inframe_codon_gain",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-06-27T11:26:22Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "SO:0001651"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-06-27T11:26:22Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -6705,78 +8483,87 @@
       "type" : "CLASS",
       "lbl" : "inframe_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000973",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000974",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000980"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001820",
       "meta" : {
         "definition" : {
-          "val" : "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.",
-          "xrefs" : [ "SO:as" ]
+          "val" : "A coding sequence variant where the change does not alter the frame of the transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Insertion_sequence"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "IS",
+          "pred" : "hasExactSynonym",
+          "val" : "inframe indel",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "insertion sequence",
+          "val" : "inframe change in CDS length",
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         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-06-27T11:25:33Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insertion_sequence"
+      "lbl" : "inframe_indel"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001820",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000973",
       "meta" : {
         "definition" : {
-          "val" : "A coding sequence variant where the change does not alter the frame of the transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats.",
+          "xrefs" : [ "SO:as" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Insertion_sequence"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "inframe indel",
+          "pred" : "hasRelatedSynonym",
+          "val" : "IS",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "inframe change in CDS length",
+          "val" : "insertion sequence",
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-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inframe_indel"
+      "lbl" : "insertion_sequence"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000970",
       "meta" : {
+        "comments" : [ "This has been obsoleted as it represents a process. replaced_by: GO:0070582" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "theta replication",
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         "basicPropertyValues" : [ {
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-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This has been obsoleted as it represents a process. replaced_by: GO:0070582"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "theta_replication"
@@ -6787,28 +8574,34 @@
           "val" : "A sequence variant where there is no resulting change to the encoded amino acid.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term." ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Silent_mutation"
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
         }, {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         }, {
-          "val" : "http://vat.gersteinlab.org/formats.php"
+          "val" : "http://en.wikipedia.org/wiki/Synonymous_mutation"
         }, {
           "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
         }, {
-          "val" : "http://en.wikipedia.org/wiki/Synonymous_mutation"
+          "val" : "http://en.wikipedia.org/wiki/Silent_mutation"
         }, {
           "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
         }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+          "val" : "http://vat.gersteinlab.org/formats.php"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:synonymous_variant",
+          "val" : "VAAST:synonymous_codon",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "synonymous codon",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "silent_mutation",
+          "pred" : "hasExactSynonym",
+          "val" : "synonymous_coding",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
@@ -6816,69 +8609,70 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAAST:synonymous_codon",
-          "xrefs" : [ ]
+          "val" : "VAT:synonymous",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "silent mutation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:synonymous_variant",
+          "val" : "silent_mutation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:synonymous_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "VEP:synonymous_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "synonymous_coding",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:synonymous SNV",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:synonymous",
+          "pred" : "hasRelatedSynonym",
+          "val" : "silent mutation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAT:synonymous",
+          "val" : "synonymous_codon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "coding-synon",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
+          "val" : "VAAST:synonymous_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "Seattleseq:synonymous-near-splice",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "synonymous_codon",
-          "xrefs" : [ ]
+          "val" : "snpEff:SYNONYMOUS_CODING",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:SYNONYMOUS_CODING",
-          "xrefs" : [ ]
+          "val" : "Seattleseq:synonymous",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "synonymous codon",
-          "xrefs" : [ ]
+          "val" : "Jannovar:synonymous_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:synonymous SNV",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
+          "pred" : "hasExactSynonym",
+          "val" : "coding-synon",
+          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-24T03:38:30Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
           "val" : "SO:0001588"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -6889,20 +8683,24 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001816",
       "meta" : {
+        "definition" : {
+          "val" : "A variant that leads to the change of an amino acid within the protein.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "non synonymous",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-24T03:33:36Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -6910,6 +8708,7 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000969",
       "meta" : {
+        "comments" : [ "This has been obsoleted as it represents a process. replaced_by: GO:0070581." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Rolling_circle"
         } ],
@@ -6919,21 +8718,20 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This has been obsoleted as it represents a process. replaced_by: GO:0070581."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "rolling_circle"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001815",
       "meta" : {
+        "definition" : {
+          "val" : "A variant that does not lead to any change in the amino acid sequence.",
+          "xrefs" : [ ]
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -6950,21 +8748,17 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000968",
       "meta" : {
+        "comments" : [ "This has been obsoleted as it represents a process. replaced_by: GO:0034961." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "sequence replication mode",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This has been obsoleted as it represents a process. replaced_by: GO:0034961."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "sequence_replication_mode"
@@ -6980,22 +8774,23 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:protein_altering_variant",
+          "val" : "protein altering variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "protein altering variant",
-          "xrefs" : [ ]
+          "val" : "VEP:protein_altering_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-24T03:38:02Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -7008,62 +8803,62 @@
           "xrefs" : [ "SO:ke" ]
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-24T03:34:03Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "inframe"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001812",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000965",
       "meta" : {
         "definition" : {
-          "val" : "A region that traverses the lipid bilayer and adopts a helical secondary structure.",
-          "xrefs" : [ "PomBase:mah" ]
+          "val" : "Structural unit composed of a self-replicating, double-stranded RNA molecule.",
+          "xrefs" : [ "SO:ma" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transmembrane helix",
+          "val" : "double stranded RNA chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-06-17T12:39:46Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transmembrane_helix"
+      "lbl" : "double_stranded_RNA_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000965",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001812",
       "meta" : {
         "definition" : {
-          "val" : "Structural unit composed of a self-replicating, double-stranded RNA molecule.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A region that traverses the lipid bilayer and adopts a helical secondary structure.",
+          "xrefs" : [ "PomBase:mah" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "double stranded RNA chromosome",
+          "val" : "transmembrane helix",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-06-17T12:39:46Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "double_stranded_RNA_chromosome"
+      "lbl" : "transmembrane_helix"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001811",
       "meta" : {
@@ -7111,20 +8906,24 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001814",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute of a coding genomic variant.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "coding variant quality",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-24T03:32:25Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -7193,42 +8992,40 @@
       "type" : "CLASS",
       "lbl" : "circular_single_stranded_RNA_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000961",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001244",
       "meta" : {
-        "definition" : {
-          "val" : "Structural unit composed of a self-replicating, RNA molecule.",
-          "xrefs" : [ "SO:ma" ]
-        },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "RNA chromosome",
+          "pred" : "hasRelatedSynonym",
+          "val" : "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "RNA_chromosome"
+      "lbl" : "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001244",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000961",
       "meta" : {
+        "definition" : {
+          "val" : "Structural unit composed of a self-replicating, RNA molecule.",
+          "xrefs" : [ "SO:ma" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping",
+          "pred" : "hasExactSynonym",
+          "val" : "RNA chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping"
+      "lbl" : "RNA_chromosome"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000960",
       "meta" : {
@@ -7280,14 +9077,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-17T12:33:25Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -7320,11 +9117,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "four bp start codon",
+          "val" : "4bp start codon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "4bp start codon",
+          "val" : "four bp start codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -7341,15 +9138,13 @@
           "val" : "X has_integral_part Y if and only if: X has_part Y and Y part_of X.",
           "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
+        "comments" : [ "Example: mRNA has_integral_part CDS." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-08-19T12:01:46Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: mRNA has_integral_part CDS."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -7372,12 +9167,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-07T04:29:10Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-07T04:29:10Z"
         } ]
       },
       "type" : "CLASS",
@@ -7390,16 +9185,16 @@
           "xrefs" : [ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:recoding_stimulatory_region",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "recoding stimulatory signal",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:recoding_stimulatory_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -7417,15 +9212,26 @@
       "id" : "http://purl.obolibrary.org/obo/SO_1001267",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "stop_codon_readthrough"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00131",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001093"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001849",
       "meta" : {
@@ -7475,57 +9281,83 @@
       "type" : "CLASS",
       "lbl" : "V_DJ_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001848",
+      "id" : "http://purl.obolibrary.org/obo/BS_00137",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001097"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000517",
       "meta" : {
         "definition" : {
-          "val" : "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence.",
-          "xrefs" : [ "PMID:21673110", "PMID:7501449", "PMID:8458332" ]
+          "val" : "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "homoID",
+          "val" : "J-SPACER",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "homol D box",
+          "val" : "J spacer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-07T04:24:14Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "homol_D_box"
+      "lbl" : "J_spacer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000517",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001848",
       "meta" : {
         "definition" : {
-          "val" : "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence.",
+          "xrefs" : [ "PMID:21673110", "PMID:7501449", "PMID:8458332" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "J spacer",
+          "val" : "homoID",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "J-SPACER",
+          "val" : "homol D box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-07T04:24:14Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "J_spacer"
+      "lbl" : "homol_D_box"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00136",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001095"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000519",
       "meta" : {
@@ -7550,15 +9382,28 @@
       "type" : "CLASS",
       "lbl" : "V_DJ_J_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000998",
+      "id" : "http://purl.obolibrary.org/obo/BS_00134",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000417"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1001273",
       "meta" : {
         "definition" : {
-          "val" : "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.",
-          "xrefs" : [ "http://www.genetics.org/cgi/content/full/170/2/661" ]
+          "val" : "A non-canonical start codon of sequence CTG.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "recursive splice site",
+          "val" : "CTG start codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -7567,26 +9412,32 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recursive_splice_site"
+      "lbl" : "CTG_start_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001273",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001845",
       "meta" : {
         "definition" : {
-          "val" : "A non-canonical start codon of sequence CTG.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis.",
+          "xrefs" : [ "PMID:11073995", "PMID:8668127" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CTG start codon",
+          "val" : "DNA damage response element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-07T04:17:25Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CTG_start_codon"
+      "lbl" : "DRE"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000514",
       "meta" : {
@@ -7596,11 +9447,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "J-NONAMER",
+          "val" : "J nonamer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "J nonamer",
+          "val" : "J-NONAMER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -7611,44 +9462,35 @@
       "type" : "CLASS",
       "lbl" : "J_nonamer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001845",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000998",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis.",
-          "xrefs" : [ "PMID:11073995", "PMID:8668127" ]
+          "val" : "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons.",
+          "xrefs" : [ "http://www.genetics.org/cgi/content/full/170/2/661" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DNA damage response element",
+          "val" : "recursive splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-07T04:17:25Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DRE"
+      "lbl" : "recursive_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000513",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000997",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A portion of a gene that is not the complete gene.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "J cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "J-CLUSTER",
+          "val" : "gene fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -7657,76 +9499,79 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "J_cluster"
+      "lbl" : "gene_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000997",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001272",
       "meta" : {
+        "definition" : {
+          "val" : "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Could be a cross product with Gene ontology, GO:0006388." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene fragment",
+          "val" : "pre-tRNA intron",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "tRNA intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_fragment"
+      "lbl" : "tRNA_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001844",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000513",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast).",
-          "xrefs" : [ "PMID:10593913", "PMID:9188496", "PMID:9211922" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "copper-response element",
+          "val" : "J-CLUSTER",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "J cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-07T04:02:51Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CuRE"
+      "lbl" : "J_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001272",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001844",
       "meta" : {
         "definition" : {
-          "val" : "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast).",
+          "xrefs" : [ "PMID:10593913", "PMID:9188496", "PMID:9211922" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pre-tRNA intron",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "tRNA intron",
+          "val" : "copper-response element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Could be a cross product with Gene ontology, GO:0006388."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-07T04:02:51Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tRNA_intron"
+      "lbl" : "CuRE"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000516",
       "meta" : {
@@ -7734,11 +9579,8 @@
           "val" : "A non functional descendant of a transcript, part of a pseudogene.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations." ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_RNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "pseudogenic transcript",
           "xrefs" : [ ]
@@ -7746,11 +9588,12 @@
           "pred" : "hasExactSynonym",
           "val" : "INSDC_qualifier:pseudo",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_RNA",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -7772,12 +9615,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-07T04:22:06Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -7789,15 +9632,13 @@
           "val" : "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease.",
           "xrefs" : [ "PMID:9301331", "SO:ma" ]
         },
+        "comments" : [ "Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "archaeal intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -7805,19 +9646,24 @@
       "type" : "CLASS",
       "lbl" : "archaeal_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000515",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000999",
       "meta" : {
         "definition" : {
-          "val" : "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A region of sequence from the end of a BAC clone that may provide a highly specific marker.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Keith Boroevich December, 2006." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "J heptamer",
+          "val" : "BAC end",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "J-HEPTAMER",
+          "val" : "BES",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "BAC end sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -7826,37 +9672,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "J_heptamer"
+      "lbl" : "BAC_end"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000999",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000515",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence from the end of a BAC clone that may provide a highly specific marker.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "BAC end sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "BES",
+          "val" : "J-HEPTAMER",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "BAC end",
+          "val" : "J heptamer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Keith Boroevich December, 2006."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "BAC_end"
+      "lbl" : "J_heptamer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001846",
       "meta" : {
@@ -7870,14 +9709,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-07T04:20:01Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -7888,23 +9727,22 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "stop_codon_redefinition_as_pyrrolysine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001277",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000994",
       "meta" : {
         "definition" : {
-          "val" : "The recoding stimulatory signal located downstream of the recoding site.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that has a known consensus sequence.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "DO not obsolete without considering MGED mapping." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime recoding site",
+          "val" : "consensus region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -7913,25 +9751,26 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_recoding_site"
+      "lbl" : "consensus_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000994",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001277",
       "meta" : {
+        "definition" : {
+          "val" : "The recoding stimulatory signal located downstream of the recoding site.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "consensus region",
+          "val" : "three prime recoding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "DO not obsolete without considering MGED mapping."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "consensus_region"
+      "lbl" : "three_prime_recoding_site"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001841",
       "meta" : {
@@ -7939,23 +9778,21 @@
           "val" : "A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error.",
           "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "JAX:hd" ]
         },
+        "comments" : [ "This terms is used by Ensembl and Vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "polymorphic psuedogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This terms is used by Ensembl and Vega. Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-07T03:46:57Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -7983,19 +9820,6 @@
       },
       "type" : "CLASS",
       "lbl" : "VD_gene_segment"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000993",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "consensus"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001840",
       "meta" : {
@@ -8003,21 +9827,22 @@
           "val" : "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G).",
           "xrefs" : [ "PMID:8321208" ]
         },
+        "comments" : [ "Changed to is_a SO:0001055 transcriptional_cis_regulatory_region from core_eukaryotic_promoter_element SO:0001660 after Ruth Lovering from GREEKC initiative pointed out that GATA boxes are frequently in enhancer regions, Dave Sant Aug 2020. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "GATA element",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "GATA box",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "GATA element",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-07T03:42:05Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -8025,31 +9850,66 @@
       },
       "type" : "CLASS",
       "lbl" : "GATA_box"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000993",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence produced from an aligment algorithm that uses multiple sequences as input.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "consensus"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001843",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.",
-          "xrefs" : [ "PMID:11483355", "PMID:11483993" ]
+          "val" : "MERGED DEFINITION:\nTARGET DEFINITION: A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors.\n--------------------\nSOURCE DEFINITION: A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components.",
+          "xrefs" : [ "PMID:11483355", "PMID:11483993", "PMID:15448137" ]
         },
+        "comments" : [ "New synonym Atf1/Pcr1 recognition motif added in response to Antonia Lock GitHub Issue Request #437, PMID:15716492" ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "M26 binding site",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "cyclic AMP response element",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m26 site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "M26_binding_site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Atf1/Pcr1 recognition motif",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "ATF/CRE site",
           "xrefs" : [ "PMID:11483993" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-07T03:58:48Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001900"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-07T03:58:48Z"
         } ]
       },
       "type" : "CLASS",
@@ -8068,24 +9928,6 @@
       },
       "type" : "CLASS",
       "lbl" : "retron"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000996",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "predicted gene",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "predicted_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000512",
       "meta" : {
@@ -8106,18 +9948,16 @@
       "type" : "CLASS",
       "lbl" : "inversion_derived_deficiency_plus_aneuploid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001274",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000996",
       "meta" : {
         "definition" : {
-          "val" : "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031" ]
+          "val" : "A region of the genome that has been predicted to be a gene but has not been confirmed by laboratory experiments.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/SECIS_element"
-        } ],
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SECIS element",
+          "val" : "predicted gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -8126,50 +9966,54 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SECIS_element"
+      "lbl" : "predicted_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000995",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001842",
       "meta" : {
+        "definition" : {
+          "val" : "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors.",
+          "xrefs" : [ "PMID:1899230", "PMID:3034432", "PMID:3125983" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "consensus mRNA",
+          "val" : "AP-1 binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "DO not obsolete without considering MGED mapping."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-07T03:54:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "consensus_mRNA"
+      "lbl" : "AP_1_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001842",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001274",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors.",
-          "xrefs" : [ "PMID:1899230", "PMID:3034432", "PMID:3125983" ]
+          "val" : "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/SECIS_element"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "AP-1 binding site",
+          "val" : "SECIS element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-07T03:54:52Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "AP_1_binding_site"
+      "lbl" : "SECIS_element"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000511",
       "meta" : {
@@ -8179,11 +10023,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "J-C-CLUSTER",
+          "val" : "J C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "J C cluster",
+          "val" : "J-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -8193,6 +10037,26 @@
       },
       "type" : "CLASS",
       "lbl" : "J_C_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000995",
+      "meta" : {
+        "definition" : {
+          "val" : "An mRNA sequence produced from an aligment algorithm that uses multiple sequences as input.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "DO not obsolete without considering MGED mapping." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "consensus mRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "consensus_mRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000990",
       "meta" : {
@@ -8200,15 +10064,13 @@
           "val" : "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.",
           "xrefs" : [ "PMID:15333696" ]
         },
+        "comments" : [ "Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "class I RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -8237,15 +10099,17 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000992",
       "meta" : {
+        "definition" : {
+          "val" : "A region of DNA that has been inserted into the bacterial genome using a bacterial artificial chromosome.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Requested by Andy Schroder - Flybase Harvard, Nov 2006." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "BAC cloned genomic insert",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Andy Schroder - Flybase Harvard, Nov 2006."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -8259,19 +10123,17 @@
           "val" : "DNA located in the genome and able to be transmitted to the offspring.",
           "xrefs" : [ "BCS:etrwz" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gDNA",
+          "val" : "genomic DNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "genomic DNA",
+          "val" : "gDNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -8284,12 +10146,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2009-08-19T02:27:04Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "PROPERTY",
@@ -8305,6 +10167,19 @@
       },
       "type" : "PROPERTY",
       "lbl" : "similar_to"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00140",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001099"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#finishes",
       "meta" : {
@@ -8312,15 +10187,13 @@
           "val" : "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary.",
           "xrefs" : [ "PMID:20226267" ]
         },
+        "comments" : [ "Example: stop_codon finishes CDS." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: stop_codon finishes CDS."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2010-10-14T02:17:53Z"
@@ -8329,27 +10202,57 @@
       "type" : "PROPERTY",
       "lbl" : "finishes"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000507",
+      "id" : "http://purl.obolibrary.org/obo/BS_00144",
       "meta" : {
-        "definition" : {
-          "val" : "A non functional descendant of an exon, part of a pseudogene.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "pseudogenic exon",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001074"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00143",
+      "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations."
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001102"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "pseudogenic_exon"
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00142",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001101"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00141",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001100"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001838",
       "meta" : {
@@ -8357,27 +10260,58 @@
           "val" : "An insertion the sequence of which cannot be mapped to the reference genome.",
           "xrefs" : [ "NCBI:th" ]
         },
+        "comments" : [ "Requested by the NCBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "novel sequence insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by the NCBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-04T01:14:50Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "novel_sequence_insertion"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000507",
+      "meta" : {
+        "definition" : {
+          "val" : "A non functional descendant of an exon, part of a pseudogene.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "pseudogenic exon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "novel_sequence_insertion"
+      "lbl" : "pseudogenic_exon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00148",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001128"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001837",
       "meta" : {
@@ -8385,6 +10319,7 @@
           "val" : "A kind of insertion where the inserted sequence is a mobile element.",
           "xrefs" : [ "EBI:dvga" ]
         },
+        "comments" : [ "Requested by the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "mobile element insertion",
@@ -8393,19 +10328,29 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-04T12:36:52Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by the EBI."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-04T12:36:52Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "mobile_element_insertion"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00147",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001081"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000506",
       "meta" : {
@@ -8415,11 +10360,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "D DJ J C cluster",
+          "val" : "D-(DJ)-J-C-CLUSTER",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "D-(DJ)-J-C-CLUSTER",
+          "val" : "D DJ J C cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -8452,6 +10397,19 @@
       },
       "type" : "CLASS",
       "lbl" : "D_J_C_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00146",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001096"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000508",
       "meta" : {
@@ -8475,6 +10433,19 @@
       },
       "type" : "CLASS",
       "lbl" : "D_DJ_J_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00145",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001073"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001839",
       "meta" : {
@@ -8501,37 +10472,36 @@
       "type" : "CLASS",
       "lbl" : "CSL_response_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000503",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000987",
       "meta" : {
+        "definition" : {
+          "val" : "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.",
+          "xrefs" : [ "SO:cb" ]
+        },
+        "comments" : [ "Attributes added to describe the different kinds of replicon. SO workshop, September 2006." ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "two-ended",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alternately_spliced_gene_encodeing_one_transcript"
+      "lbl" : "linear"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001262",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000503",
       "meta" : {
-        "definition" : {
-          "val" : "An attribute describing a translational frameshift of -1.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "minus 1 translationally frameshifted",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "minus_1_translationally_frameshifted"
+      "lbl" : "alternately_spliced_gene_encodeing_one_transcript"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001834",
       "meta" : {
@@ -8545,40 +10515,37 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-09-01T03:29:41Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "C_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000987",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001262",
       "meta" : {
         "definition" : {
-          "val" : "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "An attribute describing a translational frameshift of -1.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "two-ended",
+          "pred" : "hasExactSynonym",
+          "val" : "minus 1 translationally frameshifted",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Attributes added to describe the different kinds of replicon. SO workshop, September 2006."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "linear"
+      "lbl" : "minus_1_translationally_frameshifted"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001833",
       "meta" : {
@@ -8588,22 +10555,22 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V region",
+          "val" : "INSDC_feature:V_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:V_region",
+          "val" : "V region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-09-01T03:28:40Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-09-01T03:28:40Z"
         } ]
       },
       "type" : "CLASS",
@@ -8611,6 +10578,11 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000986",
       "meta" : {
+        "definition" : {
+          "val" : "The attribute of whether a nucleotide polymer is linear or circular.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Attributes added to describe the different kinds of replicon. SO workshop, September 2006." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "topology attribute",
@@ -8619,34 +10591,10 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Attributes added to describe the different kinds of replicon. SO workshop, September 2006."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "topology_attribute"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000502",
-      "meta" : {
-        "definition" : {
-          "val" : "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "transcribed_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001261",
       "meta" : {
@@ -8667,24 +10615,22 @@
       "type" : "CLASS",
       "lbl" : "recoded_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000989",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000502",
       "meta" : {
         "definition" : {
-          "val" : "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.",
-          "xrefs" : [ "PMID:15333696" ]
+          "val" : "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "class II RNA",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "class_II_RNA"
+      "lbl" : "transcribed_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001836",
       "meta" : {
@@ -8702,14 +10648,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-09-01T03:52:05Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -8746,11 +10692,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "internal Shine Dalgarno sequence",
+          "val" : "internal Shine-Dalgarno sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "internal Shine-Dalgarno sequence",
+          "val" : "internal Shine Dalgarno sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -8760,6 +10706,25 @@
       },
       "type" : "CLASS",
       "lbl" : "internal_Shine_Dalgarno_sequence"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000989",
+      "meta" : {
+        "definition" : {
+          "val" : "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm.",
+          "xrefs" : [ "PMID:15333696" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "class II RNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "class_II_RNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001835",
       "meta" : {
@@ -8777,11 +10742,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-09-01T03:50:16Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-09-01T03:50:16Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -8819,21 +10784,43 @@
           "val" : "A quality of a nucleotide polymer that has no terminal nucleotide residues.",
           "xrefs" : [ "SO:cb" ]
         },
+        "comments" : [ "Attributes added to describe the different kinds of replicon. SO workshop, September 2006." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "zero-ended",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Attributes added to describe the different kinds of replicon. SO workshop, September 2006."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "circular"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00149",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000419"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1001266",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "stop_codon_redefinition_as_selenocysteine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001830",
       "meta" : {
@@ -8841,6 +10828,7 @@
           "val" : "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments.",
           "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience June, 2011." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism"
         } ],
@@ -8866,37 +10854,26 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-07-14T12:12:35Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-07-14T12:12:35Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience June, 2011."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "AFLP_fragment"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001266",
-      "meta" : {
-        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stop_codon_redefinition_as_selenocysteine"
+      "lbl" : "AFLP_fragment"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000983",
       "meta" : {
+        "definition" : {
+          "val" : "The attribute of how many strands are present in a nucleotide polymer.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Attributes added to describe the different kinds of replicon. SO workshop, September 2006." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "strand attribute",
@@ -8905,9 +10882,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Attributes added to describe the different kinds of replicon. SO workshop, September 2006."
         } ]
       },
       "type" : "CLASS",
@@ -8915,6 +10889,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000982",
       "meta" : {
+        "definition" : {
+          "val" : "A transcription terminator that is not dependent upon Rho. Rather, the mRNA contains a sequence that allows it to base-pair with itself and make a stem-loop structure.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "rho independent bacterial terminator",
@@ -8946,19 +10924,6 @@
       },
       "type" : "CLASS",
       "lbl" : "mRNA_recoded_by_codon_redefinition"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000985",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Attributes added to describe the different kinds of replicon. SO workshop, September 2006."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "double"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000501",
       "meta" : {
@@ -8978,25 +10943,6 @@
       },
       "type" : "CLASS",
       "lbl" : "reverse_Hoogsteen_base_pair"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001264",
-      "meta" : {
-        "definition" : {
-          "val" : "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mRNA recoded by translational bypass",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "mRNA_recoded_by_translational_bypass"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001832",
       "meta" : {
@@ -9012,54 +10958,50 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-09-01T03:27:20Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-09-01T03:27:20Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "immunoglobulin_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001831",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001264",
       "meta" : {
         "definition" : {
-          "val" : "A match to a protein HMM such as pfam.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "protein hmm match",
+          "val" : "mRNA recoded by translational bypass",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-08-11T03:20:27Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "protein_hmm_match"
+      "lbl" : "mRNA_recoded_by_translational_bypass"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000984",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000985",
       "meta" : {
+        "definition" : {
+          "val" : "When a nucleotide polymer has two strands that are reverse-complement to one another and pair together.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Attributes added to describe the different kinds of replicon. SO workshop, September 2006." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Attributes added to describe the different kinds of replicon. SO workshop, September 2006."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "single"
+      "lbl" : "double"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001263",
       "meta" : {
@@ -9079,6 +11021,31 @@
       },
       "type" : "CLASS",
       "lbl" : "plus_1_translationally_frameshifted"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001831",
+      "meta" : {
+        "definition" : {
+          "val" : "A match to a protein HMM such as pfam.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "protein hmm match",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-08-11T03:20:27Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "protein_hmm_match"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000500",
       "meta" : {
@@ -9101,6 +11068,21 @@
       },
       "type" : "CLASS",
       "lbl" : "Hoogsteen_base_pair"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000984",
+      "meta" : {
+        "definition" : {
+          "val" : "When a nucleotide polymer has only one strand.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Attributes added to describe the different kinds of replicon. SO workshop, September 2006." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "single"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001870",
       "meta" : {
@@ -9114,11 +11096,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-01-17T03:09:35Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -9156,6 +11138,7 @@
           "val" : "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome.",
           "xrefs" : [ "NCBI:th", "PMID:18564416" ]
         },
+        "comments" : [ "NCBI definition: An orphan rearrangement between chromosomal location observed in isolation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "rearrangement region",
@@ -9164,39 +11147,16 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "NCBI definition: An orphan rearrangement between chromosomal location observed in isolation."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-02-03T04:38:35Z"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "rearrangement_region"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001871",
-      "meta" : {
-        "definition" : {
-          "val" : "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle.",
-          "xrefs" : [ "GO:mah", "PMID:12411492" ]
-        },
-        "basicPropertyValues" : [ {
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-01-17T03:14:02Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "PCB"
+      "lbl" : "rearrangement_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000540",
       "meta" : {
@@ -9206,11 +11166,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DJ J C cluster",
+          "val" : "(DJ)-J-C-CLUSTER",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "(DJ)-J-C-CLUSTER",
+          "val" : "DJ J C cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -9220,6 +11180,26 @@
       },
       "type" : "CLASS",
       "lbl" : "DJ_J_C_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001871",
+      "meta" : {
+        "definition" : {
+          "val" : "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle.",
+          "xrefs" : [ "GO:mah", "PMID:12411492" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-01-17T03:14:02Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "PCB"
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#gained",
       "meta" : {
@@ -9227,18 +11207,16 @@
           "val" : "X gained Y if X is a variant_of X' and Y part of X but not X'.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-06-28T12:51:10Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "PROPERTY",
@@ -9252,11 +11230,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DJ C cluster",
+          "val" : "(DJ)-C-CLUSTER",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "(DJ)-C-CLUSTER",
+          "val" : "DJ C cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -9273,19 +11251,17 @@
           "val" : "A gene suspected of being involved in the expression of a trait.",
           "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience December, 2011." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "candidate gene",
+          "val" : "target gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "target gene",
+          "val" : "candidate gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience December, 2011."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
@@ -9328,23 +11304,21 @@
           "val" : "A contig of BAC reads.",
           "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience December, 2011." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "BAC read contig",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-01-17T02:45:04Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience December, 2011."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-01-17T02:45:04Z"
         } ]
       },
       "type" : "CLASS",
@@ -9358,11 +11332,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-J-C-CLUSTER",
+          "val" : "V J C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V J C cluster",
+          "val" : "V-J-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -9373,115 +11347,111 @@
       "type" : "CLASS",
       "lbl" : "V_J_C_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000538",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001869",
       "meta" : {
         "definition" : {
-          "val" : "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A candidate gene whose function has something in common biologically with the trait under investigation.",
+          "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience December, 2011." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V gene recombination feature",
+          "val" : "functional target gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V-RS",
+          "val" : "functional candidate gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-01-17T02:57:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "V_gene_recombination_feature"
+      "lbl" : "functional_candidate_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001869",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000538",
       "meta" : {
         "definition" : {
-          "val" : "A candidate gene whose function has something in common biologically with the trait under investigation.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "functional candidate gene",
+          "val" : "V-RS",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "functional target gene",
+          "val" : "V gene recombination feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience December, 2011."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-01-17T02:57:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "functional_candidate_gene"
+      "lbl" : "V_gene_recombination_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000537",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001868",
       "meta" : {
         "definition" : {
-          "val" : "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A candidate gene whose association with a trait is based on the gene's location on a chromosome.",
+          "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience December, 2011." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "V-SPACER",
+          "pred" : "hasRelatedSynonym",
+          "val" : "positional target gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V spacer",
+          "val" : "positional candidate gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-01-17T02:54:42Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "V_spacer"
+      "lbl" : "positional_candidate_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001868",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000537",
       "meta" : {
         "definition" : {
-          "val" : "A candidate gene whose association with a trait is based on the gene's location on a chromosome.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "positional candidate gene",
+          "val" : "V spacer",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "positional target gene",
+          "pred" : "hasExactSynonym",
+          "val" : "V-SPACER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience December, 2011."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-01-17T02:54:42Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "positional_candidate_gene"
+      "lbl" : "V_spacer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000532",
       "meta" : {
@@ -9518,14 +11488,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-19T03:56:54Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -9537,6 +11507,7 @@
           "val" : "A dinucleotide repeat region composed of GT repeating elements.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "paper:PMID:16043634." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "d(GT)n",
@@ -9546,14 +11517,11 @@
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "paper:PMID:16043634."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-19T03:54:37Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-19T03:54:37Z"
         } ]
       },
       "type" : "CLASS",
@@ -9600,12 +11568,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-20T10:12:19Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -9619,11 +11587,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-J-CLUSTER",
+          "val" : "V J cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V J cluster",
+          "val" : "V-J-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -9642,11 +11610,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-HEPTAMER",
+          "val" : "V heptamer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V heptamer",
+          "val" : "V-HEPTAMER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -9671,41 +11639,16 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-19T04:24:16Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "Sap1_recognition_motif"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001861",
-      "meta" : {
-        "definition" : {
-          "val" : "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs.",
-          "xrefs" : [ "GO:mah", "PMID:11111080", "PMID:16537923" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "SRE",
-          "xrefs" : [ "GO:mah" ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-19T03:02:05Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-19T04:24:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sterol_regulatory_element"
+      "lbl" : "Sap1_recognition_motif"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000530",
       "meta" : {
@@ -9748,6 +11691,31 @@
       },
       "type" : "CLASS",
       "lbl" : "three_prime_stem_loop_structure"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001861",
+      "meta" : {
+        "definition" : {
+          "val" : "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs.",
+          "xrefs" : [ "GO:mah", "PMID:11111080", "PMID:16537923" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "SRE",
+          "xrefs" : [ "GO:mah" ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-19T03:02:05Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "sterol_regulatory_element"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001860",
       "meta" : {
@@ -9755,15 +11723,13 @@
           "val" : "A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). The S. pombe telomeric repeat consensus is TTAC(0-1)A(0-1)G(1-8).",
           "xrefs" : [ "ISBN:978-0199638901", "PMID:9016645" ]
         },
+        "comments" : [ "Page 208 of ISBN:978-0199638901" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "rDIS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Page 208 of ISBN:978-0199638901"
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
@@ -9785,11 +11751,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-D-(DJ)-J-C-CLUSTER",
+          "val" : "V D DJ J C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V D DJ J C cluster",
+          "val" : "V-D-(DJ)-J-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -9837,12 +11803,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-14T10:25:02Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-14T10:25:02Z"
         } ]
       },
       "type" : "CLASS",
@@ -9870,6 +11836,32 @@
       },
       "type" : "CLASS",
       "lbl" : "V_D_DJ_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00125",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001082"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00124",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000839"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000525",
       "meta" : {
@@ -9879,11 +11871,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-(VJ)-J-CLUSTER",
+          "val" : "V VJ J cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V VJ J cluster",
+          "val" : "V-(VJ)-J-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -9894,48 +11886,49 @@
       "type" : "CLASS",
       "lbl" : "V_VJ_J_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001856",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001284",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels.",
-          "xrefs" : [ "PMID:16963626" ]
+          "val" : "A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products.",
+          "xrefs" : [ "ISBN:0198506732", "PMID:32665585" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "CCAAT motif",
-          "xrefs" : [ ]
+        "comments" : [ "Definition updated with Mejia-Almonte et.al PMID:32665585 on Aug 5, 2020. Added relationship has_part SO:0002300" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Regulon"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-10T05:13:54Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CCAAT_motif"
+      "lbl" : "regulon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001284",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001856",
       "meta" : {
         "definition" : {
-          "val" : "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal.",
-          "xrefs" : [ "ISBN:0198506732" ]
+          "val" : "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels.",
+          "xrefs" : [ "PMID:16963626" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Regulon"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "CCAAT motif",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-10T05:13:54Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regulon"
+      "lbl" : "CCAAT_motif"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001855",
       "meta" : {
@@ -9951,16 +11944,29 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-10T05:09:45Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-10T05:09:45Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "MCB"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00129",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001063"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000524",
       "meta" : {
@@ -9970,11 +11976,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-(VJ)-CLUSTER",
+          "val" : "V VJ cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V VJ cluster",
+          "val" : "V-(VJ)-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -10039,14 +12045,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-10T05:22:13Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -10070,6 +12076,19 @@
       },
       "type" : "CLASS",
       "lbl" : "UAG_stop_codon_signal"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00128",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001071"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001857",
       "meta" : {
@@ -10083,11 +12102,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-10T05:19:10Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -10095,29 +12114,6 @@
       },
       "type" : "CLASS",
       "lbl" : "Ace2_UAS"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000526",
-      "meta" : {
-        "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "V-CLUSTER",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "V cluster",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "V_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001281",
       "meta" : {
@@ -10138,33 +12134,28 @@
       "type" : "CLASS",
       "lbl" : "flanking_three_prime_quadruplet_recoding_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001852",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000526",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc.",
-          "xrefs" : [ "PMID:9233811" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mating type M-box",
+          "val" : "V-CLUSTER",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "V cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-10-07T04:39:43Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mating_type_M_box"
+      "lbl" : "V_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001288",
       "meta" : {
@@ -10172,6 +12163,7 @@
           "val" : "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding.",
           "xrefs" : [ "PMID:12519954", "SO:ke" ]
         },
+        "comments" : [ "This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "stop codon signal",
@@ -10180,9 +12172,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal."
         } ]
       },
       "type" : "CLASS",
@@ -10210,6 +12199,32 @@
       },
       "type" : "CLASS",
       "lbl" : "V_VDJ_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001852",
+      "meta" : {
+        "definition" : {
+          "val" : "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc.",
+          "xrefs" : [ "PMID:9233811" ]
+        },
+        "comments" : [ "Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "mating type M-box",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-10-07T04:39:43Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "mating_type_M_box"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_1001287",
       "meta" : {
@@ -10236,6 +12251,7 @@
           "val" : "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron.",
           "xrefs" : [ "PMID:11956219", "PMID:17211681" ]
         },
+        "comments" : [ "The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "IDP (GATA)",
@@ -10246,14 +12262,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-07T04:32:42Z"
@@ -10285,15 +12298,19 @@
       "type" : "CLASS",
       "lbl" : "V_VDJ_C_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001286",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000523",
       "meta" : {
         "definition" : {
-          "val" : "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.",
-          "xrefs" : [ "PMID:12519954", "SO:ke" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime repeat recoding signal",
+          "val" : "V VJ C cluster",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "V-(VJ)-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -10302,7 +12319,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_repeat_recoding_signal"
+      "lbl" : "V_VJ_C_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001854",
       "meta" : {
@@ -10311,41 +12328,56 @@
           "xrefs" : [ "PMID:18806792" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "single molecule fish probe",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "smFISH probe",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "single molecule fish probe",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-10T05:00:30Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "smFISH_probe"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000523",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001286",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements.",
+          "xrefs" : [ "PMID:12519954", "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V VJ C cluster",
+          "val" : "three prime repeat recoding signal",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "three_prime_repeat_recoding_signal"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1001285",
+      "meta" : {
+        "definition" : {
+          "val" : "A stop codon signal for a UGA stop codon redefinition.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-(VJ)-C-CLUSTER",
+          "val" : "UGA stop codon signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -10354,7 +12386,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "V_VJ_C_cluster"
+      "lbl" : "UGA_stop_codon_signal"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001853",
       "meta" : {
@@ -10364,22 +12396,22 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ARE",
+          "val" : "androgen response element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "androgen response element",
+          "val" : "ARE",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2011-10-10T04:52:44Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -10392,31 +12424,12 @@
           "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "V VDJ J cluster",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "V-(VDJ)-J-CLUSTER",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "V_VDJ_J_cluster"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001285",
-      "meta" : {
-        "definition" : {
-          "val" : "A stop codon signal for a UGA stop codon redefinition.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "UGA stop codon signal",
+          "val" : "V VDJ J cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -10425,7 +12438,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "UGA_stop_codon_signal"
+      "lbl" : "V_VDJ_J_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001892",
       "meta" : {
@@ -10433,6 +12446,7 @@
           "val" : "A feature amplification of a region containing a transcription factor binding site.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "xrefs" : [ {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
@@ -10442,25 +12456,23 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:TFBS_amplification",
+          "val" : "TFBS amplification ",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "TFBS amplification ",
-          "xrefs" : [ ]
+          "val" : "VEP:TFBS_amplification",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-03T12:42:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-03T12:42:48Z"
         } ]
       },
       "type" : "CLASS",
@@ -10473,12 +12485,35 @@
           "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "HEPTAMER",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "heptamer of recombination feature of vertebrate immune system gene",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "heptamer_of_recombination_feature_of_vertebrate_immune_system_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000560",
+      "meta" : {
+        "definition" : {
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "D J cluster",
+          "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "HEPTAMER",
+          "pred" : "hasExactSynonym",
+          "val" : "D-J-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -10487,7 +12522,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "heptamer_of_recombination_feature_of_vertebrate_immune_system_gene"
+      "lbl" : "D_J_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001891",
       "meta" : {
@@ -10495,48 +12530,43 @@
           "val" : "A feature amplification of a region containing a regulatory region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "xrefs" : [ {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "VEP:regulatory_region_amplification",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "regulatory region amplification",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T12:41:28Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "regulatory_region_amplification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000560",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000563",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A 12 or 23 nucleotide spacer between two regions of an immunoglobulin/T-cell receptor gene that may be rearranged by recombinase.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "D-J-CLUSTER",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "D J cluster",
+          "val" : "vertebrate immune system gene recombination spacer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -10545,7 +12575,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "D_J_cluster"
+      "lbl" : "vertebrate_immune_system_gene_recombination_spacer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001410",
       "meta" : {
@@ -10558,14 +12588,14 @@
           "pred" : "hasExactSynonym",
           "val" : "experimental_output_artefact",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "experimental output artefact",
-          "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "analysis feature",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "experimental output artefact",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -10581,49 +12611,33 @@
           "val" : "A feature ablation whereby the deleted region includes a regulatory region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "xrefs" : [ {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:regulatory_region_ablation",
+          "val" : "regulatory region ablation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "regulatory region ablation",
-          "xrefs" : [ ]
+          "val" : "VEP:regulatory_region_ablation",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-03T12:45:13Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-03T12:45:13Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "regulatory_region_ablation"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000563",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "vertebrate immune system gene recombination spacer",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "vertebrate_immune_system_gene_recombination_spacer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001893",
       "meta" : {
@@ -10631,34 +12645,34 @@
           "val" : "A feature ablation whereby the deleted region includes a transcript feature.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "xrefs" : [ {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:transcript_ablation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "VEP:transcript_ablation",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "transcript ablation",
-          "xrefs" : [ ]
+          "val" : "Jannovar:transcript_ablation",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:transcript_ablation",
+          "val" : "transcript ablation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T12:44:19Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
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       },
       "type" : "CLASS",
@@ -10666,6 +12680,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000562",
       "meta" : {
+        "definition" : {
+          "val" : "Nine nucleotide recombination site, part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "nonamer of recombination feature of vertebrate immune system gene",
@@ -10685,23 +12703,21 @@
           "val" : "A feature fusion where the deletion brings together a regulatory region and a transcript region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "transcript regulatory region fusion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T12:40:17Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
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       },
       "type" : "CLASS",
@@ -10746,84 +12762,84 @@
       "type" : "CLASS",
       "lbl" : "cleaved_for_gpi_anchor_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001889",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001405",
       "meta" : {
         "definition" : {
-          "val" : "A feature amplification of a region containing a transcript.",
+          "val" : "A post translationally modified tyrosine amino acid feature.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+          "val" : "MOD:00919"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:transcript_amplification",
+          "val" : "ModTry",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "modified L tyrosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "transcript amplification",
+          "val" : "modified L-tyrosine",
           "xrefs" : [ ]
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         "basicPropertyValues" : [ {
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_amplification"
+      "lbl" : "modified_L_tyrosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000558",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001889",
       "meta" : {
         "definition" : {
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-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A feature amplification of a region containing a transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
+        "xrefs" : [ {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "C-CLUSTER",
-          "xrefs" : [ ]
+          "val" : "VEP:transcript_amplification",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "C cluster",
+          "val" : "transcript amplification",
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         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-03T12:39:23Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "C_cluster"
+      "lbl" : "transcript_amplification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001405",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000558",
       "meta" : {
         "definition" : {
-          "val" : "A post translationally modified tyrosine amino acid feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
-        "xrefs" : [ {
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-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L tyrosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ModTry",
+          "val" : "C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-tyrosine",
+          "val" : "C-CLUSTER",
           "xrefs" : [ ]
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         "basicPropertyValues" : [ {
@@ -10832,7 +12848,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_L_tyrosine"
+      "lbl" : "C_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001404",
       "meta" : {
@@ -10845,15 +12861,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L proline",
+          "val" : "modified L-proline ",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "ModPro",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-proline ",
+          "val" : "modified L proline",
           "xrefs" : [ ]
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         "basicPropertyValues" : [ {
@@ -10870,6 +12887,7 @@
           "val" : "A fusion where the deletion brings together transcription factor binding sites.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "TFBS fusion ",
@@ -10880,14 +12898,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-03T12:36:42Z"
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
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-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -10900,15 +12915,15 @@
       "meta" : {
         "definition" : {
           "val" : "3'-most region of a precursor transcript that is clipped off during processing.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime clip",
+          "val" : "3'-clip",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "3'-clip",
+          "val" : "three prime clip",
           "xrefs" : [ ]
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         "basicPropertyValues" : [ {
@@ -10941,11 +12956,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "D-CLUSTER",
+          "val" : "D cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "D cluster",
+          "val" : "D-CLUSTER",
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         "basicPropertyValues" : [ {
@@ -10968,7 +12983,8 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "ModArg",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "modified L arginine",
@@ -10985,6 +13001,48 @@
       },
       "type" : "CLASS",
       "lbl" : "modified_L_arginine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001401",
+      "meta" : {
+        "definition" : {
+          "val" : "A post translationally modified leucine amino acid feature.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "MOD:00911"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "modified L leucine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ModLeu",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "modified L-leucine ",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
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+      },
+      "type" : "CLASS",
+      "lbl" : "modified_L_leucine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000554",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "assortment_derived_deficiency_plus_duplication"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001885",
       "meta" : {
@@ -10992,6 +13050,7 @@
           "val" : "A feature translocation where the region contains a transcription factor binding site.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "transcription factor binding site translocation",
@@ -11002,43 +13061,41 @@
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         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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-          "val" : "sequence"
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-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
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       },
       "type" : "CLASS",
       "lbl" : "TFBS_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001401",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001400",
       "meta" : {
         "definition" : {
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+          "val" : "A post translationally modified lysine amino acid feature.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "MOD:00911"
+          "val" : "MOD:00912"
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         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L leucine",
+          "val" : "modified L lysine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModLeu",
+          "val" : "modified L-lysine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-leucine ",
-          "xrefs" : [ ]
+          "val" : "ModLys",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
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@@ -11046,20 +13103,7 @@
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-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "assortment_derived_deficiency_plus_duplication"
+      "lbl" : "modified_L_lysine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001884",
       "meta" : {
@@ -11067,23 +13111,21 @@
           "val" : "A feature translocation where the region contains a regulatory region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "regulatory region translocation",
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       },
       "type" : "CLASS",
@@ -11093,32 +13135,32 @@
       "meta" : {
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-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:polyA_site",
+          "val" : "polyA site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polyA cleavage site",
+          "val" : "INSDC_feature:polyA_site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "polyA junction",
+          "pred" : "hasRelatedSynonym",
+          "val" : "polyadenylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polyA site",
+          "val" : "polyA cleavage site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "polyA_junction",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "polyadenylation site",
+          "pred" : "hasExactSynonym",
+          "val" : "polyA junction",
           "xrefs" : [ ]
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         "basicPropertyValues" : [ {
@@ -11132,35 +13174,31 @@
       "type" : "CLASS",
       "lbl" : "polyA_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001400",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001887",
       "meta" : {
         "definition" : {
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+          "val" : "A feature fusion where the deletion brings together regulatory regions.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "MOD:00912"
-        } ],
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-lysine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "modified L lysine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ModLys",
+          "val" : "regulatory region fusion",
           "xrefs" : [ ]
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         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-03T12:35:58Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_L_lysine"
+      "lbl" : "regulatory_region_fusion"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001403",
       "meta" : {
@@ -11173,7 +13211,7 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ModVal",
+          "val" : "modified L valine",
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         }, {
           "pred" : "hasExactSynonym",
@@ -11181,8 +13219,9 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L valine",
-          "xrefs" : [ ]
+          "val" : "ModVal",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -11191,34 +13230,6 @@
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-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "regulatory_region_fusion"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000556",
       "meta" : {
@@ -11228,15 +13239,15 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5'RS",
+          "val" : "five prime D-recombination signal sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five prime D-recombination signal sequence",
+          "val" : "five prime D recombination signal sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five prime D recombination signal sequence",
+          "val" : "5'RS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -11253,6 +13264,7 @@
           "val" : "A feature fusion where the deletion brings together transcript regions.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "transcript fusion",
@@ -11261,9 +13273,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T12:34:56Z"
@@ -11275,19 +13284,22 @@
       "type" : "CLASS",
       "lbl" : "transcript_fusion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000555",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001402",
       "meta" : {
         "definition" : {
-          "val" : "5' most region of a precursor transcript that is clipped off during processing.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A post translationally modified selenocysteine amino acid feature.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "MOD:01158"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime clip",
+          "val" : "modified L selenocysteine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "5' clip",
+          "pred" : "hasExactSynonym",
+          "val" : "modified L-selenocysteine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -11296,24 +13308,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_clip"
+      "lbl" : "modified_L_selenocysteine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001402",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000555",
       "meta" : {
         "definition" : {
-          "val" : "A post translationally modified selenocysteine amino acid feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "5' most region of a precursor transcript that is clipped off during processing.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
-        "xrefs" : [ {
-          "val" : "MOD:01158"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "modified L selenocysteine",
+          "pred" : "hasRelatedSynonym",
+          "val" : "5' clip",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-selenocysteine",
+          "val" : "five prime clip",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -11322,7 +13331,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_L_selenocysteine"
+      "lbl" : "five_prime_clip"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001881",
       "meta" : {
@@ -11330,20 +13339,18 @@
           "val" : "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "feature translocation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T11:38:52Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -11358,6 +13365,7 @@
           "val" : "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "aneuploid chromosome",
@@ -11366,9 +13374,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila."
         } ]
       },
       "type" : "CLASS",
@@ -11380,6 +13385,7 @@
           "val" : "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "feature amplification",
@@ -11389,18 +13395,41 @@
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-03T11:37:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-03T11:37:48Z"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "feature_amplification"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001883",
+      "meta" : {
+        "definition" : {
+          "val" : "A feature translocation where the region contains a transcript.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Created in conjunction with the EBI." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transcript translocation",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-03T12:29:52Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "transcript_translocation"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000552",
       "meta" : {
@@ -11408,6 +13437,7 @@
           "val" : "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex.",
           "xrefs" : [ "SO:jh" ]
         },
+        "comments" : [ "Not found in Eukaryotic sequence." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence"
         } ],
@@ -11431,41 +13461,10 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Not found in Eukaryotic sequence."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "Shine_Dalgarno_sequence"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001883",
-      "meta" : {
-        "definition" : {
-          "val" : "A feature translocation where the region contains a transcript.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "transcript translocation",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-03T12:29:52Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "transcript_translocation"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001882",
       "meta" : {
@@ -11473,20 +13472,18 @@
           "val" : "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "feature fusion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T11:39:20Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -11499,14 +13496,11 @@
       "meta" : {
         "definition" : {
           "val" : "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "poly(A) signal",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "INSDC_qualifier:polyA_signal_sequence",
           "xrefs" : [ ]
@@ -11522,6 +13516,10 @@
           "pred" : "hasExactSynonym",
           "val" : "polyadenylation termination signal",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "poly(A) signal",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -11537,20 +13535,18 @@
           "val" : "A sequence variant that falls entirely or partially within a genomic feature.",
           "xrefs" : [ "EBI:fc", "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "feature alteration",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T11:27:27Z"
@@ -11577,38 +13573,20 @@
       },
       "type" : "CLASS",
       "lbl" : "inversion_derived_bipartite_duplication"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000546",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "designed sequence",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "designed_sequence"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001877",
       "meta" : {
         "definition" : {
-          "val" : "A non-coding RNA over 200nucleotides in length.",
+          "val" : "A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced.",
           "xrefs" : [ "HGNC:mw" ]
         },
+        "comments" : [ "Updated the definition of lncRNA (SO:0001877) from \"A non-coding RNA over 200nucleotides in length.\" to \"A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced.\" See GitHub Issue #575" ],
         "xrefs" : [ {
           "val" : "http://www.gencodegenes.org/gencode_biotypes.html"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lncRNA_transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "long non-coding RNA",
+          "val" : "INSDC_qualifier:lncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasBroadSynonym",
@@ -11616,22 +13594,45 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:lncRNA",
+          "val" : "long non-coding RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "lncRNA_transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-02-14T05:18:01Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "lncRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000546",
+      "meta" : {
+        "definition" : {
+          "val" : "An oligonucleotide sequence that was designed by an experimenter that may or may not correspond with any natural sequence.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "designed sequence",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lnc_RNA"
+      "lbl" : "designed_sequence"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000549",
       "meta" : {
@@ -11658,6 +13659,7 @@
           "val" : "A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "feature ablation",
@@ -11666,15 +13668,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T11:36:48Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -11729,10 +13728,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "alternately_spliced_gene_encoding_greater_than_one_transcript"
@@ -11772,14 +13769,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-02-03T04:43:45Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -11791,7 +13788,12 @@
           "val" : "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's.",
           "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience January, 2012." ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "partial genomic sequence assembly",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "sequence assembly with N-gaps",
           "xrefs" : [ ]
@@ -11799,20 +13801,13 @@
           "pred" : "hasBroadSynonym",
           "val" : "pseudomolecule",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "partial genomic sequence assembly",
-          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-02-14T05:05:32Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience January, 2012."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-02-14T05:05:32Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -11868,6 +13863,7 @@
           "val" : "A supercontig that is not been assigned to any ultracontig during a genome assembly project.",
           "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience January, 2012." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "unassigned supercontig",
@@ -11878,21 +13874,31 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience January, 2012."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-02-14T05:02:20Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "unassigned_supercontig"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001430",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000553"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000583",
       "meta" : {
@@ -11902,11 +13908,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pre edited region",
+          "val" : "pre-edited region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "pre-edited region",
+          "val" : "pre edited region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -11938,6 +13944,7 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001432",
       "meta" : {
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "mutation affecting polyadenylation",
@@ -11948,18 +13955,13 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "SO:0001545"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "sequence_variant_affecting_polyadenylation"
@@ -11976,11 +13978,11 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transposon",
+          "val" : "transposable element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "transposable element",
+          "val" : "transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -11993,6 +13995,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000585",
       "meta" : {
+        "definition" : {
+          "val" : "snoRNA that is associated with guiding methylation of nucleotides. It contains two short conserved sequence motifs: C (RUGAUGA) near the 5-prime end and D (CUGA) near the 3-prime end.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "C/D box snoRNA encoding",
@@ -12006,26 +14012,15 @@
       "type" : "CLASS",
       "lbl" : "C_D_box_snoRNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000584",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001431",
       "meta" : {
         "definition" : {
-          "val" : "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023" ]
+          "val" : "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/TmRNA"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "10Sa RNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:tmRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ssrA",
+          "val" : "cryptic gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12034,17 +14029,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tmRNA"
+      "lbl" : "cryptic_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001431",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000100",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A proviral gene with origin endogenous retrovirus.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cryptic gene",
+          "val" : "endogenous retroviral gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12053,17 +14048,28 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cryptic_gene"
+      "lbl" : "endogenous_retroviral_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000100",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000584",
       "meta" : {
         "definition" : {
-          "val" : "A proviral gene with origin endogenous retrovirus.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/TmRNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "endogenous retroviral gene",
+          "val" : "INSDC_feature:tmRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "10Sa RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ssrA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12072,7 +14078,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "endogenous_retroviral_gene"
+      "lbl" : "tmRNA"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000581",
       "meta" : {
@@ -12121,6 +14127,7 @@
           "val" : "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence.",
           "xrefs" : [ "RFAM:jd" ]
         },
+        "comments" : [ "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "cis regulatory frameshift element",
@@ -12134,15 +14141,16 @@
       "type" : "CLASS",
       "lbl" : "cis_regulatory_frameshift_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000579",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001426",
       "meta" : {
         "definition" : {
-          "val" : "A locatable feature on a transcript that is edited.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A read produced by the polymerase based sequence by synthesis method.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "An example is a read produced by Illumina technology." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "edited transcript feature",
+          "pred" : "hasRelatedSynonym",
+          "val" : "polymerase synthesis read",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12151,29 +14159,26 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edited_transcript_feature"
+      "lbl" : "polymerase_synthesis_read"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001426",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000579",
       "meta" : {
         "definition" : {
-          "val" : "A read produced by the polymerase based sequence by synthesis method.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A locatable feature on a transcript that is edited.",
+          "xrefs" : [ "SO:ma" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "polymerase synthesis read",
+          "pred" : "hasExactSynonym",
+          "val" : "edited transcript feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An example is a read produced by Illumina technology."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polymerase_synthesis_read"
+      "lbl" : "edited_transcript_feature"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001429",
       "meta" : {
@@ -12200,21 +14205,38 @@
           "val" : "A sequence assembly derived from expressed sequences.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "From tracker [ 2372385 ] expressed_sequence_assembly." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "expressed sequence assembly",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "From tracker [ 2372385 ] expressed_sequence_assembly."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "expressed_sequence_assembly"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001423",
+      "meta" : {
+        "definition" : {
+          "val" : "A read produced by the dye terminator method of sequencing.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "dye terminator read",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "dye_terminator_read"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000576",
       "meta" : {
@@ -12224,11 +14246,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VJ gene",
+          "val" : "V-J-GENE",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V-J-GENE",
+          "val" : "VJ gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12239,15 +14261,16 @@
       "type" : "CLASS",
       "lbl" : "VJ_gene_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001423",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001422",
       "meta" : {
         "definition" : {
-          "val" : "A read produced by the dye terminator method of sequencing.",
+          "val" : "A region of a polypeptide, involved in the transition from one conformational state to another.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "dye terminator read",
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide conformational switch",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12256,35 +14279,36 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dye_terminator_read"
+      "lbl" : "conformational_switch"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001422",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000575",
       "meta" : {
         "definition" : {
-          "val" : "A region of a polypeptide, involved in the transition from one conformational state to another.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that can be transcribed into a small cytoplasmic RNA (scRNA).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide conformational switch",
+          "val" : "scRNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conformational_switch"
+      "lbl" : "scRNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000575",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000578",
       "meta" : {
+        "definition" : {
+          "val" : "A region that can be transcribed into a small nucleolar RNA (snoRNA).",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "scRNA encoding",
+          "val" : "snoRNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12293,7 +14317,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "scRNA_encoding"
+      "lbl" : "snoRNA_encoding"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001425",
       "meta" : {
@@ -12301,15 +14325,13 @@
           "val" : "A read produced by ligation based sequencing technologies.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "An example of this kind of read is one produced by ABI SOLiD." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "ligation based read",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An example of this kind of read is one produced by ABI SOLiD."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -12317,11 +14339,16 @@
       "type" : "CLASS",
       "lbl" : "ligation_based_read"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000578",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001424",
       "meta" : {
+        "definition" : {
+          "val" : "A read produced by pyrosequencing technology.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "An example is a read produced by Roche 454 technology." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "snoRNA encoding",
+          "pred" : "hasRelatedSynonym",
+          "val" : "pyorsequenced read",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12330,7 +14357,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "snoRNA_encoding"
+      "lbl" : "pyrosequenced_read"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000577",
       "meta" : {
@@ -12354,28 +14381,6 @@
       },
       "type" : "CLASS",
       "lbl" : "centromere"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001424",
-      "meta" : {
-        "definition" : {
-          "val" : "A read produced by pyrosequencing technology.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "pyorsequenced read",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An example is a read produced by Roche 454 technology."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "pyrosequenced_read"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000572",
       "meta" : {
@@ -12402,6 +14407,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000571",
       "meta" : {
+        "definition" : {
+          "val" : "A region that can be transcribed into a microRNA (miRNA).",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "miRNA encoding",
@@ -12446,11 +14455,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-D-J-GENE",
+          "val" : "VDJ gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VDJ gene",
+          "val" : "V-D-J-GENE",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12483,6 +14492,10 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000573",
       "meta" : {
+        "definition" : {
+          "val" : "A region that can be transcribed into a ribosomal RNA (rRNA).",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "rRNA encoding",
@@ -12504,11 +14517,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3'D-RS",
+          "val" : "three prime D recombination signal sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "three prime D recombination signal sequence",
+          "val" : "3'D-RS",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -12549,18 +14562,16 @@
           "val" : "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "GO:0003964 RNA-directed DNA polymerase activity." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Retrotransposed"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "GO:0003964 RNA-directed DNA polymerase activity."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0100042"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0100042"
         } ]
       },
       "type" : "CLASS",
@@ -12614,23 +14625,21 @@
           "val" : "A repeat region which is part of the regional centromere outer repeat region.",
           "xrefs" : [ "PMID:16407326", "SO:vw" ]
         },
+        "comments" : [ "For the S. pombe project - requested by Val Wood." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "dh repeat",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-06T11:50:07Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "For the S. pombe project - requested by Val Wood."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -12639,9 +14648,10 @@
       "id" : "http://purl.obolibrary.org/obo/SO_0000568",
       "meta" : {
         "definition" : {
-          "val" : "An unregulated promoter that allows continuous expression.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A promoter that can allow for transcription in both directions.",
+          "xrefs" : [ "PMID:21601935", "SO:ke" ]
         },
+        "comments" : [ "Definition updated in Aug 2020 by Dave Sant." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "bidirectional promoter",
@@ -12661,19 +14671,17 @@
           "val" : "An experimental region, defined by a tiling array experiment to be transcribed at some level.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Term requested by the MODencode group." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "transfrag",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "transcribed fragment",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "transfrag",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term requested by the MODencode group."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -12704,30 +14712,25 @@
       "type" : "CLASS",
       "lbl" : "three_prime_flanking_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001896",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001412",
       "meta" : {
         "definition" : {
-          "val" : "A CDS that is part of a transposable element.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.",
+          "xrefs" : [ "PMID:32782014", "SO:cb" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transposable element CDS",
+          "val" : "topologically defined region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-05T01:57:04Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transposable_element_CDS"
+      "lbl" : "topologically_defined_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000565",
       "meta" : {
@@ -12737,11 +14740,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-(VDJ)-J-C-CLUSTER",
+          "val" : "V VDJ J C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V VDJ J C cluster",
+          "val" : "V-(VDJ)-J-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12752,16 +14755,49 @@
       "type" : "CLASS",
       "lbl" : "V_VDJ_J_C_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001412",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001896",
       "meta" : {
         "definition" : {
-          "val" : "A region that is defined according to its relations with other regions within the same sequence.",
+          "val" : "A CDS that is part of a transposable element.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transposable element CDS",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-05T01:57:04Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "transposable_element_CDS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001411",
+      "meta" : {
+        "definition" : {
+          "val" : "A region defined by its disposition to be involved in a biological process.",
           "xrefs" : [ "SO:cb" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "topologically defined region",
+          "val" : "INSDC_note:biological_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "biological region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_misc_feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12770,7 +14806,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "topologically_defined_region"
+      "lbl" : "biological_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001895",
       "meta" : {
@@ -12778,34 +14814,33 @@
           "val" : "A feature ablation whereby the deleted region includes a transcription factor binding site.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Created in conjunction with the EBI." ],
         "xrefs" : [ {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcription factor binding site ablation",
+          "val" : "TFBS ablation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "TFBS ablation",
+          "val" : "transcription factor binding site ablation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "VEP:TFBS_ablation",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2012-04-03T12:45:56Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Created in conjunction with the EBI."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -12818,40 +14853,12 @@
           "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "V DJ J C cluster",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "V-(DJ)-J-C-CLUSTER",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "V_DJ_J_C_cluster"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001411",
-      "meta" : {
-        "definition" : {
-          "val" : "A region defined by its disposition to be involved in a biological process.",
-          "xrefs" : [ "SO:cb" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "biological region",
-          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:biological_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_misc_feature",
+          "val" : "V DJ J C cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12860,7 +14867,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "biological_region"
+      "lbl" : "V_DJ_J_C_cluster"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001898",
       "meta" : {
@@ -12868,6 +14875,7 @@
           "val" : "A repeat region which is part of the regional centromere outer repeat region.",
           "xrefs" : [ "PMID:16407326", "SO:vw" ]
         },
+        "comments" : [ "For the S. pombe project - requested by Val Wood." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "dg repeat",
@@ -12882,23 +14890,20 @@
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "For the S. pombe project - requested by Val Wood."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "dg_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000567",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001414",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.",
-          "xrefs" : [ "FB:km" ]
+          "val" : "The point within a chromosome where a insertion begins or ends.",
+          "xrefs" : [ "SO:cb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inversion derived aneuploid chromosome",
+          "val" : "insertion breakpoint",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12907,17 +14912,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inversion_derived_aneuploid_chromosome"
+      "lbl" : "insertion_breakpoint"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001414",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000567",
       "meta" : {
         "definition" : {
-          "val" : "The point within a chromosome where a insertion begins or ends.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion.",
+          "xrefs" : [ "FB:km" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insertion breakpoint",
+          "val" : "inversion derived aneuploid chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12926,7 +14931,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insertion_breakpoint"
+      "lbl" : "inversion_derived_aneuploid_chromosome"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001413",
       "meta" : {
@@ -12959,14 +14964,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-05T04:09:45Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-05T04:09:45Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
@@ -12980,11 +14985,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "V-(VJ)-J-C-CLUSTER",
+          "val" : "V VJ J C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V VJ J C cluster",
+          "val" : "V-(VJ)-J-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -12995,21 +15000,51 @@
       "type" : "CLASS",
       "lbl" : "V_VJ_J_C_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001452",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002300",
       "meta" : {
+        "definition" : {
+          "val" : "Transcription units or transcribed coding sequences.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
+        },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H",
+          "val" : "unit of gene expression",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "unit_of_gene_expression"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001452",
+      "meta" : {
+        "definition" : {
+          "val" : "A positively charged, hydorophilic amino acid encoded by the codons CAT and CAC.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "His",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -13023,17 +15058,18 @@
           "val" : "A single stranded oligo used for polymerase chain reaction.",
           "xrefs" : [ "http://mged.sourceforge.net/ontologies/MGEDontology.php" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "forward primer oligo",
+          "val" : "forward primer polynucleotide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DNA forward primer",
+          "val" : "forward DNA primer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "forward primer polynucleotide",
+          "val" : "forward primer oligo",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -13041,23 +15077,20 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "forward DNA primer",
+          "val" : "DNA forward primer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "forward primer sequence",
+          "val" : "forward primer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "forward primer",
+          "val" : "forward primer sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
         } ]
       },
       "type" : "CLASS",
@@ -13069,6 +15102,7 @@
           "val" : "A primary transcript that, at least in part, encodes one or more proteins.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "May contain introns." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
@@ -13082,9 +15116,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "May contain introns."
         } ]
       },
       "type" : "CLASS",
@@ -13092,25 +15123,55 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001451",
       "meta" : {
+        "definition" : {
+          "val" : "A positively charged, hydorophilic amino acid encoded by the codons CGN (CGT, CGC, CGA and CGG), AGA and AGG.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Arg",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "R",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "arginine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002301",
+      "meta" : {
+        "definition" : {
+          "val" : "DNA regions delimited by different nonspurious TSS-TTS pairs.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
+        },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transcription unit",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "arginine"
+      "lbl" : "transcription_unit"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000123",
       "meta" : {
@@ -13118,6 +15179,7 @@
           "val" : "An attribute describing a gene that is regulated at transcription.",
           "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "By:<protein_id>." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "transcriptionally regulated",
@@ -13126,9 +15188,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "By:<protein_id>."
         } ]
       },
       "type" : "CLASS",
@@ -13136,39 +15195,54 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001454",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "E",
+        "definition" : {
+          "val" : "A negatively charged, hydorophilic amino acid encoded by the codons GAA and GAG.",
           "xrefs" : [ ]
-        }, {
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Glu",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "glutamic acid",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "E",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
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-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "glutamic_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000122",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001453",
       "meta" : {
         "definition" : {
-          "val" : "A folded RNA sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A negatively charged, hydorophilic amino acid encoded by the codons GAT and GAC.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA sequence secondary structure",
+          "val" : "Asp",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "D",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "aspartic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -13177,49 +15251,46 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_sequence_secondary_structure"
+      "lbl" : "aspartic_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001453",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000122",
       "meta" : {
+        "definition" : {
+          "val" : "A folded RNA sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "D",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "aspartic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Asp",
+          "val" : "RNA sequence secondary structure",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "aspartic_acid"
+      "lbl" : "RNA_sequence_secondary_structure"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001450",
       "meta" : {
+        "definition" : {
+          "val" : "A positively charged, hydorophilic amino acid encoded by the codons AAA and AAG.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Lys",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "K",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
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         } ]
@@ -13248,19 +15319,23 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001449",
       "meta" : {
+        "definition" : {
+          "val" : "A polar, hydorophilic amino acid encoded by the codons AAT and AAC.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "Asn",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "N",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
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@@ -13271,31 +15346,33 @@
       "id" : "http://purl.obolibrary.org/obo/SO_0000117",
       "meta" : {
         "basicPropertyValues" : [ {
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-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "transcript_with_readthrough_stop_codon"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001448",
       "meta" : {
+        "definition" : {
+          "val" : "A polar, hydorophilic amino acid encoded by the codons CAA and CAG. ",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Gln",
-          "xrefs" : [ ]
+          "val" : "Q",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Q",
-          "xrefs" : [ ]
+          "val" : "Gln",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
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         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
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-        }, {
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         } ]
@@ -13319,43 +15396,29 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001445",
       "meta" : {
+        "definition" : {
+          "val" : "A polar, hydorophilic amino acid encoded by the codons ACN (ACT, ACC, ACA and ACG).",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Thr",
-          "xrefs" : [ ]
+          "val" : "T",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "T",
-          "xrefs" : [ ]
+          "val" : "Thr",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
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         "basicPropertyValues" : [ {
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-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "threonine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000598",
-      "meta" : {
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-        "basicPropertyValues" : [ {
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-      },
-      "type" : "CLASS",
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     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000114",
       "meta" : {
@@ -13393,90 +15456,86 @@
       "type" : "CLASS",
       "lbl" : "methylated_cytosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000113",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000598",
       "meta" : {
-        "definition" : {
-          "val" : "A viral sequence which has integrated into a host genome.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
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-          "val" : "proviral region",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "proviral sequence",
+          "val" : "transcript_edited_by_C-insertion_and_dinucleotide_insertion",
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         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "proviral_region"
+      "lbl" : "edited_by_C_insertion_and_dinucleotide_insertion"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000597",
+      "meta" : {
+        "definition" : {
+          "val" : "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.",
+          "xrefs" : [ "http://www.rna.ucla.edu/index.html" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "transcript_edited_by_U_insertion/deletion"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001444",
       "meta" : {
+        "definition" : {
+          "val" : "A polar, hydorophilic amino acid encoded by the codons TCN (TCT, TCC, TCA, TCG), AGT and AGC.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "S",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "Ser",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
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         "basicPropertyValues" : [ {
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-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "serine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000597",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000113",
       "meta" : {
         "definition" : {
-          "val" : "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.",
-          "xrefs" : [ "http://www.rna.ucla.edu/index.html" ]
+          "val" : "A viral sequence which has integrated into a host genome.",
+          "xrefs" : [ "SO:ke" ]
         },
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-      "type" : "CLASS",
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-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001447",
-      "meta" : {
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Cys",
+          "val" : "proviral region",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "C",
+          "pred" : "hasRelatedSynonym",
+          "val" : "proviral sequence",
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         "basicPropertyValues" : [ {
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-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cysteine"
+      "lbl" : "proviral_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000116",
       "meta" : {
@@ -13492,23 +15551,53 @@
       "type" : "CLASS",
       "lbl" : "edited"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001446",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001447",
       "meta" : {
+        "definition" : {
+          "val" : "A polar amino acid encoded by the codons TGT and TGC.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Y",
-          "xrefs" : [ ]
+          "val" : "Cys",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Tyr",
-          "xrefs" : [ ]
+          "val" : "C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cysteine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001446",
+      "meta" : {
+        "definition" : {
+          "val" : "A polar, hydorophilic amino acid encoded by the codons TAT and TAC.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Tyr",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
+          "pred" : "hasExactSynonym",
+          "val" : "Y",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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@@ -13519,10 +15608,8 @@
         "basicPropertyValues" : [ {
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-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "edited_by_C_to_U_substitution"
@@ -13530,12 +15617,10 @@
       "id" : "http://purl.obolibrary.org/obo/SO_0000115",
       "meta" : {
         "basicPropertyValues" : [ {
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-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "transcript_feature"
@@ -13548,8 +15633,8 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "located sequence feature",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_note:sequence_feature",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -13557,11 +15642,11 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence feature",
+          "val" : "INSDC_feature:misc_feature",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:sequence_feature",
+          "pred" : "hasRelatedSynonym",
+          "val" : "located sequence feature",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -13569,7 +15654,7 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:misc_feature",
+          "val" : "sequence feature",
           "xrefs" : [ ]
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@@ -13586,17 +15671,22 @@
           "val" : "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains.",
           "xrefs" : [ "http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html" ]
         },
+        "comments" : [ "Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "H/ACA box snoRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "box H/ACA snoRNA",
+          "val" : "H ACA box snoRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H ACA box snoRNA",
+          "val" : "SNORA",
+          "xrefs" : [ "PMID:31828325" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "box H/ACA snoRNA",
           "xrefs" : [ ]
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@@ -13609,47 +15699,29 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001441",
       "meta" : {
+        "definition" : {
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codons TTT and TTC.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "F",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "Phe",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
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-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "phenylalanine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001440",
-      "meta" : {
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-          "val" : "W",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Trp",
-          "xrefs" : [ ]
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-      },
-      "type" : "CLASS",
-      "lbl" : "tryptophan"
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       "id" : "http://purl.obolibrary.org/obo/SO_0000593",
       "meta" : {
@@ -13657,19 +15729,24 @@
           "val" : "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.",
           "xrefs" : [ "http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html" ]
         },
+        "comments" : [ "Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "box C/D snoRNA",
+          "val" : "C/D box snoRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "C/D box snoRNA",
-          "xrefs" : [ ]
+          "val" : "SNORD",
+          "xrefs" : [ "PMID:31828325" ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "C D box snoRNA",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "box C/D snoRNA",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -13679,16 +15756,23 @@
       "type" : "CLASS",
       "lbl" : "C_D_box_snoRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000596",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001440",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a small nucleolar RNA of the box H/ACA family.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codon TGG.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H ACA box snoRNA primary transcript",
-          "xrefs" : [ ]
+          "val" : "Trp",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "W",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -13696,7 +15780,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H_ACA_box_snoRNA_primary_transcript"
+      "lbl" : "tryptophan"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000112",
       "meta" : {
@@ -13710,15 +15794,15 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "primer oligonucleotide",
+          "val" : "DNA primer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DNA primer",
+          "val" : "primer polynucleotide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "primer polynucleotide",
+          "val" : "primer oligonucleotide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -13733,49 +15817,50 @@
       "type" : "CLASS",
       "lbl" : "primer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001443",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000596",
       "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding a small nucleolar RNA of the box H/ACA family.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "G",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Gly",
+          "val" : "H ACA box snoRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "glycine"
+      "lbl" : "H_ACA_box_snoRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001442",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001443",
       "meta" : {
+        "definition" : {
+          "val" : "A non-polar, hydorophilic amino acid encoded by the codons GGN (GGT, GGC, GGA and GGG).",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Met",
-          "xrefs" : [ ]
+          "val" : "G",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "M",
-          "xrefs" : [ ]
+          "val" : "Gly",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "methionine"
+      "lbl" : "glycine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000111",
       "meta" : {
@@ -13814,6 +15899,32 @@
       },
       "type" : "CLASS",
       "lbl" : "C_D_box_snoRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001442",
+      "meta" : {
+        "definition" : {
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codon ATG.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Met",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "M",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "methionine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000590",
       "meta" : {
@@ -13823,16 +15934,12 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "SRP RNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
           "val" : "7S RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:SRP_RNA",
+          "val" : "SRP RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
@@ -13842,6 +15949,10 @@
           "pred" : "hasBroadSynonym",
           "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:SRP_RNA",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -13859,7 +15970,7 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H-type pseudoknot",
+          "val" : "hairpin-type pseudoknot",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -13867,11 +15978,11 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "classical pseudoknot",
+          "val" : "H-type pseudoknot",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "hairpin-type pseudoknot",
+          "val" : "classical pseudoknot",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -13903,12 +16014,23 @@
       "type" : "CLASS",
       "lbl" : "pseudoknot"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000107",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001438",
       "meta" : {
+        "definition" : {
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codons ATH (ATT, ATC and ATA).",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequencing primer",
-          "xrefs" : [ ]
+          "val" : "I",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ile",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -13916,58 +16038,57 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequencing_primer"
+      "lbl" : "isoleucine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001438",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000107",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "Ile",
+        "definition" : {
+          "val" : "A single stranded oligo used for polymerase chain reaction.",
           "xrefs" : [ ]
-        }, {
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "I",
+          "val" : "sequencing primer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "isoleucine"
+      "lbl" : "sequencing_primer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000106",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "non_capped_primary_transcript"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001437",
       "meta" : {
+        "definition" : {
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codons CTN (CTT, CTC, CTA and CTG), TTA and TTG.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Leu",
-          "xrefs" : [ ]
+          "val" : "L",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "L",
-          "xrefs" : [ ]
+          "val" : "Leu",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -13990,10 +16111,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "sequence_variant_obs"
@@ -14027,19 +16146,23 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001439",
       "meta" : {
+        "definition" : {
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codons CCN (CCT, CCC, CCA and CCG).",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "P",
-          "xrefs" : [ ]
+          "val" : "Pro",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Pro",
-          "xrefs" : [ ]
+          "val" : "P",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -14053,19 +16176,17 @@
           "val" : "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by the Trypanosome community." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "cassette type psedogene",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "cassette pseudogene",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "cassette type psedogene",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by the Trypanosome community."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -14079,6 +16200,7 @@
           "val" : "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions.",
           "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028" ]
         },
+        "comments" : [ "GO:0000372." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Group_I_intron"
@@ -14091,9 +16213,6 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "GO:0000372."
         } ]
       },
       "type" : "CLASS",
@@ -14118,6 +16237,26 @@
       },
       "type" : "CLASS",
       "lbl" : "clone_insert_end"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000102",
+      "meta" : {
+        "definition" : {
+          "val" : "A match to an EST or cDNA sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "expressed sequence match",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "expressed_sequence_match"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000586",
       "meta" : {
@@ -14126,16 +16265,16 @@
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "tmRNA primary transcript",
+          "pred" : "hasRelatedSynonym",
+          "val" : "ssrA RNA primary transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
           "val" : "10Sa RNA primary transcript",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ssrA RNA primary transcript",
+          "pred" : "hasExactSynonym",
+          "val" : "tmRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14165,16 +16304,15 @@
       "type" : "CLASS",
       "lbl" : "three_prime_RACE_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000102",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000105",
       "meta" : {
         "definition" : {
-          "val" : "A match to an EST or cDNA sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.",
+          "xrefs" : [ "http://www.medterms.com/script/main/art.asp?articlekey=5152" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "expressed sequence match",
+          "val" : "chromosome arm",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14183,18 +16321,25 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "expressed_sequence_match"
+      "lbl" : "chromosome_arm"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000589",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001436",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a signal recognition particle RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codons GTN (GTT, GTC, GTA and GTG).",
+          "xrefs" : [ ]
         },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SRP RNA primary transcript",
-          "xrefs" : [ ]
+          "val" : "V",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Val",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -14202,17 +16347,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SRP_RNA_primary_transcript"
+      "lbl" : "valine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000105",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000589",
       "meta" : {
         "definition" : {
-          "val" : "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere.",
-          "xrefs" : [ "http://www.medterms.com/script/main/art.asp?articlekey=5152" ]
+          "val" : "A primary transcript encoding a signal recognition particle RNA.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromosome arm",
+          "val" : "SRP RNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14221,29 +16366,34 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosome_arm"
+      "lbl" : "SRP_RNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001436",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000104",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Polypeptide"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Val",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "V",
+          "val" : "protein",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0000358"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "valine"
+      "lbl" : "polypeptide"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000588",
       "meta" : {
@@ -14253,16 +16403,16 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:autocatalytically_spliced_intron",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "autocatalytically spliced intron",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:autocatalytically_spliced_intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14273,101 +16423,106 @@
       "type" : "CLASS",
       "lbl" : "autocatalytically_spliced_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000104",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001435",
       "meta" : {
         "definition" : {
-          "val" : "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A non-polar, hydorophobic amino acid encoded by the codons GCN (GCT, GCC, GCA and GCG).",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Polypeptide"
-        } ],
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "protein",
-          "xrefs" : [ ]
+          "val" : "Ala",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0000358"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide"
+      "lbl" : "alanine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001435",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002322",
       "meta" : {
+        "definition" : {
+          "val" : "A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Ala",
+          "val" : "stop gained-NMD escaping",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "A",
+          "val" : "stop gained variant-nonsense-mediated decay escaping",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alanine"
+      "lbl" : "stop_gained_NMD_escaping"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001474",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000143",
       "meta" : {
         "definition" : {
-          "val" : "The boundary between the spliced leader and the first exon of the mRNA.",
+          "val" : "A region of known length which may be used to manufacture a longer region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "trans-splice junction",
+          "val" : "assembly component",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-07-13T04:50:49Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trans_splice_junction"
+      "lbl" : "assembly_component"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000143",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001474",
       "meta" : {
         "definition" : {
-          "val" : "A region of known length which may be used to manufacture a longer region.",
+          "val" : "The boundary between the spliced leader and the first exon of the mRNA.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "assembly component",
+          "val" : "trans-splice junction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-07-13T04:50:49Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "assembly_component"
+      "lbl" : "trans_splice_junction"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001473",
       "meta" : {
@@ -14401,6 +16556,36 @@
       },
       "type" : "CLASS",
       "lbl" : "miRNA_antiguide"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002323",
+      "meta" : {
+        "definition" : {
+          "val" : "A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "frameshift variant-nonsense-mediated decay triggering",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "frameshift variant-NMD triggering",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "frameshift_variant_NMD_triggering"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000142",
       "meta" : {
@@ -14440,43 +16625,60 @@
       "type" : "CLASS",
       "lbl" : "recoded_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001476",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002320",
       "meta" : {
         "definition" : {
-          "val" : "A plasmid that occurs naturally.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence variant that leads to a change in the location of a termination codon in a transcript but allows the transcript to escape nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants.",
+          "xrefs" : [ "GenCC:AR" ]
         },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "natural plasmid",
+          "val" : "NMD escaping variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "nonsense-mediated decay escaping variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-09-01T03:43:06Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "natural_plasmid"
+      "lbl" : "NMD_escaping_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000144",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001476",
       "meta" : {
+        "definition" : {
+          "val" : "A plasmid that occurs naturally.",
+          "xrefs" : [ "SO:xp" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "natural plasmid",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-09-01T03:43:06Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "primary_transcript_attribute"
+      "lbl" : "natural_plasmid"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001475",
       "meta" : {
@@ -14497,6 +16699,47 @@
       },
       "type" : "CLASS",
       "lbl" : "outron"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002321",
+      "meta" : {
+        "definition" : {
+          "val" : "A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated decay (NMD).",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "stop gained-NMD triggering",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stop gained variant-nonsense-mediated decay triggering",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "stop_gained_NMD_triggering"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000144",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "primary_transcript_attribute"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001470",
       "meta" : {
@@ -14521,17 +16764,14 @@
       "meta" : {
         "definition" : {
           "val" : "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Terminator_(genetics)"
         } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "INSDC_qualifier:terminator",
           "xrefs" : [ ]
@@ -14539,6 +16779,10 @@
           "pred" : "hasExactSynonym",
           "val" : "terminator sequence",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -14566,6 +16810,25 @@
       },
       "type" : "CLASS",
       "lbl" : "primer_match"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001471",
+      "meta" : {
+        "definition" : {
+          "val" : "A match against an RST sequence.",
+          "xrefs" : [ "SO:nlw" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "RST match",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "RST_match"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000140",
       "meta" : {
@@ -14578,10 +16841,6 @@
           "val" : "http://en.wikipedia.org/wiki/Attenuator"
         } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "attenuator sequence",
           "xrefs" : [ ]
@@ -14589,6 +16848,10 @@
           "pred" : "hasExactSynonym",
           "val" : "INSDC_qualifier:attenuator",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -14598,24 +16861,35 @@
       "type" : "CLASS",
       "lbl" : "attenuator"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001471",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002319",
       "meta" : {
         "definition" : {
-          "val" : "A match against an RST sequence.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A sequence variant that leads to a change in the location of a termination codon in a transcript that leads to nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants.",
+          "xrefs" : [ "GenCC:AR" ]
         },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RST match",
+          "val" : "nonsense-mediated decay triggering variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "NMD triggering variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-30T17:12:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RST_match"
+      "lbl" : "NMD_triggering_variant"
     }, {
       "id" : "http://purl.obolibrary.org/obo/so#homologous_to",
       "meta" : {
@@ -14636,25 +16910,111 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:ribosome_binding_site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ribosome entry site",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasBroadSynonym",
           "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "ribosome_entry_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002317",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that results in no gene product.",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "absent gene product",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-18T22:35:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "absent_gene_product"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002318",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that alters the structure of a gene product.",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501)" ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:ribosome_binding_site",
+          "val" : "altered gene product structure",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-18T22:35:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "altered_gene_product_structure"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002315",
+      "meta" : {
+        "definition" : {
+          "val" : "A variant that increases the level or amount of gene product produced.",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "increased gene product level",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ribosome entry site",
+          "val" : "increased_transcription_level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "increased transcription level",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-18T22:35:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ribosome_entry_site"
+      "lbl" : "increased_gene_product_level"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000136",
       "meta" : {
@@ -14693,6 +17053,75 @@
       },
       "type" : "CLASS",
       "lbl" : "RST"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001466",
+      "meta" : {
+        "definition" : {
+          "val" : "An UST located in the 5'UTR of a protein-coding transcript.",
+          "xrefs" : [ "SO:nlw" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "5' UST",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "five_prime_UST"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002316",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that decreases the level or amount of gene product produced.",
+          "xrefs" : [ "GenCC:AR" ]
+        },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "reduced gene product level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "reduced transcription level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "reduced_transcription_level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "reduced_gene_product_level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "decreased gene product level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "decreased transcription level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "decreased_transcription_level",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-18T22:35:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "decreased_gene_product_level"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000135",
       "meta" : {
@@ -14713,24 +17142,53 @@
       "type" : "CLASS",
       "lbl" : "maternally_imprinted"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001466",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000138",
       "meta" : {
         "definition" : {
-          "val" : "An UST located in the 5'UTR of a protein-coding transcript.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "An epigenetically modified gene, rearranged at the DNA level.",
+          "xrefs" : [ "SO:xp" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "gene rearranged at DNA level",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_rearranged_at_DNA_level"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002313",
+      "meta" : {
+        "definition" : {
+          "val" : "An element that always exists within the promoter region of a viral gene.",
+          "xrefs" : [ "GREEKC:rl" ]
         },
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "core viral promoter element",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "5' UST",
+          "val" : "general transcription factor binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_UST"
+      "lbl" : "core_viral_promoter_element"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001469",
       "meta" : {
@@ -14751,24 +17209,58 @@
       "type" : "CLASS",
       "lbl" : "five_prime_RST"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000138",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002314",
       "meta" : {
         "definition" : {
-          "val" : "An epigenetically modified gene, rearranged at the DNA level.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence variant that alters the level or amount of gene product produced. This high level term can be applied where the direction of level change (increased vs decreased gene product level) is unknown or not confirmed.",
+          "xrefs" : [ "GenCC:AR" ]
         },
+        "comments" : [ "Added as per request from Ang Roberts as part of GenCC November 2020. See Issue Request #501 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/501). Updated definition 17 Feb 2023 along with updates from GenCC. See Issue Request #612." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene rearranged at DNA level",
+          "val" : "altered gene product level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "altered_transcription_level",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "altered transcription level",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-12-18T22:35:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_rearranged_at_DNA_level"
+      "lbl" : "altered_gene_product_level"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001468",
+      "meta" : {
+        "definition" : {
+          "val" : "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.",
+          "xrefs" : [ "SO:nlw" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "3' RST",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "three_prime_RST"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000137",
       "meta" : {
@@ -14776,15 +17268,13 @@
           "val" : "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Examples are x-inactivation and immunoglobulin formation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "allelically excluded",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Examples are x-inactivation and immunoglobulin formation."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
@@ -14792,15 +17282,36 @@
       "type" : "CLASS",
       "lbl" : "allelically_excluded"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001468",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000132",
       "meta" : {
         "definition" : {
-          "val" : "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A single stranded oligo used for polymerase chain reaction.",
+          "xrefs" : [ "http://mged.sourceforge.net/ontologies/MGEDontology.php" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3' RST",
+          "val" : "reverse DNA primer",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "reverse primer sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "reverse primer oligonucleotide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "reverse primer",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DNA reverse primer",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "reverse primer oligo",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14809,7 +17320,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_RST"
+      "lbl" : "reverse_primer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001463",
       "meta" : {
@@ -14819,15 +17330,15 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "long intergenic non-coding RNA",
+          "val" : "long intervening non-coding RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "long intervening non-coding RNA",
+          "val" : "large intervening non-coding RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "large intervening non-coding RNA",
+          "val" : "long intergenic non-coding RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14838,47 +17349,78 @@
       "type" : "CLASS",
       "lbl" : "lincRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000132",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002311",
       "meta" : {
         "definition" : {
-          "val" : "A single stranded oligo used for polymerase chain reaction.",
-          "xrefs" : [ "http://mged.sourceforge.net/ontologies/MGEDontology.php" ]
+          "val" : "A regulatory_region including the Transcription Start Site (TSS) of a gene found in genes of viruses.",
+          "xrefs" : [ "GREEKC:cl" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "reverse primer",
+          "val" : "viral promoter",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "reverse primer sequence",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "reverse primer oligo",
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "viral_promoter"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002312",
+      "meta" : {
+        "definition" : {
+          "val" : "An element that always exists within the promoter region of a prokaryotic gene.",
+          "xrefs" : [ "GREEKC:rl" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "general transcription factor binding site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "reverse DNA primer",
+          "val" : "core prokaryotic promoter element",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "DNA reverse primer",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "core_prokaryotic_promoter_element"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000131",
+      "meta" : {
+        "definition" : {
+          "val" : "An attribute describing a gene that is regulated as it is translated.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "reverse primer oligonucleotide",
+          "val" : "translationally regulated",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reverse_primer"
+      "lbl" : "translationally_regulated"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001462",
       "meta" : {
@@ -14886,6 +17428,7 @@
           "val" : "A collection of contigs.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "See tracker ID: 2138359." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "contig collection",
@@ -14894,23 +17437,20 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "See tracker ID: 2138359."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "contig_collection"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000131",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001465",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a gene that is regulated as it is translated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A UST located in the 3'UTR of a protein-coding transcript.",
+          "xrefs" : [ "SO:nlw" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "translationally regulated",
+          "pred" : "hasRelatedSynonym",
+          "val" : "3' UST",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14919,7 +17459,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translationally_regulated"
+      "lbl" : "three_prime_UST"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000134",
       "meta" : {
@@ -14947,15 +17487,15 @@
       "type" : "CLASS",
       "lbl" : "genomically_imprinted"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001465",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001464",
       "meta" : {
         "definition" : {
-          "val" : "A UST located in the 3'UTR of a protein-coding transcript.",
+          "val" : "An EST spanning part or all of the untranslated regions of a protein-coding transcript.",
           "xrefs" : [ "SO:nlw" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "3' UST",
+          "pred" : "hasExactSynonym",
+          "val" : "UTR sequence tag",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -14964,7 +17504,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_UST"
+      "lbl" : "UST"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000133",
       "meta" : {
@@ -14985,24 +17525,31 @@
       "type" : "CLASS",
       "lbl" : "epigenetically_modified"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001464",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002310",
       "meta" : {
         "definition" : {
-          "val" : "An EST spanning part or all of the untranslated regions of a protein-coding transcript.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "The promoter of a cryptic gene.",
+          "xrefs" : [ "GREEKC:cl" ]
         },
+        "comments" : [ "Added by Dave to be consistent with other ontologies updated with GREEKC initiative." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "UTR sequence tag",
+          "val" : "cryptic promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "UST"
+      "lbl" : "cryptic_promoter"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000130",
       "meta" : {
@@ -15012,11 +17559,11 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "post-translationally regulated",
+          "val" : "post translationally regulated",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "post translationally regulated",
+          "val" : "post-translationally regulated",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15052,6 +17599,7 @@
           "val" : "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "See tracker ID 2060908." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "insulator binding site",
@@ -15060,46 +17608,50 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "See tracker ID 2060908."
         } ]
       },
       "type" : "CLASS",
       "lbl" : "insulator_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000129",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002308",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is silenced by DNA methylation.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "The ends of a DNA loop where the two strands of DNA are held in close physical proximity. During interphase the anchors of DNA loops are convergently oriented CTCF binding sites.",
+          "xrefs" : [ "GREEKC:cl", "PMID:32782014" ]
         },
+        "comments" : [ "Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene silenced by DNA methylation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "methylation-silenced gene",
+          "val" : "DNA loop anchor",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_silenced_by_DNA_methylation"
+      "lbl" : "DNA_loop_anchor"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000128",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000129",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is silenced by DNA modification.",
+          "val" : "A gene that is silenced by DNA methylation.",
           "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene silenced by DNA modification",
+          "val" : "gene silenced by DNA methylation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "methylation-silenced gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15108,7 +17660,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_silenced_by_DNA_modification"
+      "lbl" : "gene_silenced_by_DNA_methylation"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001459",
       "meta" : {
@@ -15136,164 +17688,187 @@
       "type" : "CLASS",
       "lbl" : "CRISPR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001456",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000128",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is silenced by DNA modification.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Pyl",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "O",
+          "val" : "gene silenced by DNA modification",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pyrrolysine"
+      "lbl" : "gene_silenced_by_DNA_modification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000125",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002309",
       "meta" : {
         "definition" : {
-          "val" : "An inducer molecule is required for transcription to occur.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An element that always exists within the promoter region of a gene. When multiple transcripts exist for a gene, the separate transcripts may have separate core_promoter_elements.",
+          "xrefs" : [ "GREEKC:rl" ]
         },
+        "comments" : [ "Added by Dave to be consistent with other ontologies updated with GREEKC initiative." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcriptionally induced",
+          "val" : "core promoter element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcriptionally_induced"
+      "lbl" : "core_promoter_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000124",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002306",
       "meta" : {
         "definition" : {
-          "val" : "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a chromosome where regulatory events occur, including epigenetic modifications. These epigenetic modifications can include nucleosome modifications and post-replicational DNA modifications.",
+          "xrefs" : [ "GREEKC:cl", "PMID:32782014" ]
         },
+        "comments" : [ "Added by Dave to be consistent with other ontologies updated with GREEKC initiative." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcriptionally constitutive",
+          "val" : "chromatin regulatory region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcriptionally_constitutive"
+      "lbl" : "chromatin_regulatory_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001455",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002307",
       "meta" : {
+        "definition" : {
+          "val" : "A region of DNA between two loop anchor positions that are held in close physical proximity.",
+          "xrefs" : [ "GREEKC:cl", "PMID:32782014" ]
+        },
+        "comments" : [ "Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Sec",
+          "val" : "DNA loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A place holder for a cross product with chebi."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "selenocysteine"
+      "lbl" : "DNA_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001458",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001456",
       "meta" : {
         "definition" : {
-          "val" : "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A relatively rare amino acid encoded by the codon UAG in some contexts, whereas UAG is a termination codon in other contexts.",
+          "xrefs" : [ "PMID:15788401" ]
         },
+        "comments" : [ "A place holder for a cross product with chebi." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "unigene cluster",
-          "xrefs" : [ ]
+          "pred" : "hasExactSynonym",
+          "val" : "Pyl",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "O",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was requested by Jeff Bowes, using the tracker, ID = 2594157."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unigene_cluster"
+      "lbl" : "pyrrolysine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000127",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002304",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is silenced.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An instance of a self-interacting DNA region flanked by left and right TAD boundaries.",
+          "xrefs" : [ "GREEKC:cl", "PMID:32782014" ]
         },
+        "comments" : [ "Added by Dave to be consistent with other ontologies updated with GREEKC initiative." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silenced gene",
+          "val" : "TAD",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "topologically associated domain",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silenced_gene"
+      "lbl" : "topologically_associated_domain"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001457",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000125",
       "meta" : {
         "definition" : {
-          "val" : "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.",
+          "val" : "An inducer molecule is required for transcription to occur.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcribed cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "unigene cluster",
+          "val" : "transcriptionally induced",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was requested by Jeff Bowes, using the tracker, ID = 2594157."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcribed_cluster"
+      "lbl" : "transcriptionally_induced"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000126",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000124",
       "meta" : {
         "definition" : {
-          "val" : "A repressor molecule is required for transcription to stop.",
+          "val" : "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcriptionally repressed",
+          "val" : "transcriptionally constitutive",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15302,12 +17877,206 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcriptionally_repressed"
+      "lbl" : "transcriptionally_constitutive"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001375",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002305",
       "meta" : {
         "definition" : {
-          "val" : "3_2prime_O_dimethyluridine is a modified uridine base feature.",
+          "val" : "A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance.",
+          "xrefs" : [ "GREEKC:cl", "PMID:32782014" ]
+        },
+        "comments" : [ "Added by Dave to be consistent with other ontologies updated with GREEKC initiative." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "TAD_boundary",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "topologically associated domain boundary",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TAD boundary",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-12T14:01:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "topologically_associated_domain_boundary"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001455",
+      "meta" : {
+        "definition" : {
+          "val" : "A relatively rare amino acid encoded by the codon UGA in some contexts, whereas UGA is a termination codon in other contexts.",
+          "xrefs" : [ "PMID:23275319" ]
+        },
+        "comments" : [ "A place holder for a cross product with chebi." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa1"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Sec",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#aa3"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "selenocysteine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000127",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene that is silenced.",
+          "xrefs" : [ "SO:xp" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "silenced gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "silenced_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002302",
+      "meta" : {
+        "definition" : {
+          "val" : "A regulon defined by considering one regulatory gene product.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
+        },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "simple regulon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "simple_regulon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001458",
+      "meta" : {
+        "definition" : {
+          "val" : "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This term was requested by Jeff Bowes, using the tracker, ID = 2594157." ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "unigene cluster",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "unigene_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002303",
+      "meta" : {
+        "definition" : {
+          "val" : "A regulon defined by considering the units of expression regulated by a specified set of regulatory gene products.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
+        },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "simple regulon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "complex_regulon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000126",
+      "meta" : {
+        "definition" : {
+          "val" : "A repressor molecule is required for transcription to stop.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transcriptionally repressed",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "transcriptionally_repressed"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001457",
+      "meta" : {
+        "definition" : {
+          "val" : "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This term was requested by Jeff Bowes, using the tracker, ID = 2594157." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transcribed cluster",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "unigene cluster",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "transcribed_cluster"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001375",
+      "meta" : {
+        "definition" : {
+          "val" : "3_2prime_O_dimethyluridine is a modified uridine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
@@ -15315,16 +18084,17 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3,2'-O-dimethyluridine",
+          "val" : "three two prime O dimethyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "three two prime O dimethyluridine",
+          "val" : "3,2'-O-dimethyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "m3Um",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -15333,6 +18103,35 @@
       },
       "type" : "CLASS",
       "lbl" : "three_two_prime_O_dimethyluridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002223",
+      "meta" : {
+        "definition" : {
+          "val" : "Sequences that decrease interactions between biological regions, such as between a promoter, its 5' context and/or the translational unit(s) it regulates. Spacers can affect regulation of translation, transcription, and other biological processes.",
+          "xrefs" : [ "PMID:20843779", "PMID:24933158", "PMID:27034378", "PMID:28422998" ]
+        },
+        "comments" : [ "Updated by Evan Christensen on May 27, 2021 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/494" ],
+        "xrefs" : [ {
+          "val" : "BioRXiv:https://doi.org/10.1101/584664"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "Inert DNA Spacer",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-09-06T19:05:52Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "inert_DNA_spacer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000044",
       "meta" : {
@@ -15359,7 +18158,12 @@
           "val" : "A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail.",
           "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Please not the synonym R psi M uses the spelled out form of the greek letter." ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "retropseudogene",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasBroadSynonym",
           "val" : "INSDC_feature:gene",
           "xrefs" : [ ]
@@ -15367,17 +18171,13 @@
           "pred" : "hasRelatedSynonym",
           "val" : "R psi G",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "pseudogene by reverse transcription",
-          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "processed pseudogene",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "retropseudogene",
+          "pred" : "hasRelatedSynonym",
+          "val" : "pseudogene by reverse transcription",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -15385,15 +18185,42 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Please not the synonym R psi M uses the spelled out form of the greek letter."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
       "lbl" : "processed_pseudogene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002224",
+      "meta" : {
+        "definition" : {
+          "val" : "A region that codes for a 2A self-cleaving polypeptide region, which is a region that can result in a break in the peptide sequence at its terminal G-P junction.",
+          "xrefs" : [ "PMID:22301656", "PMID:28526819" ]
+        },
+        "comments" : [ "Added by Dave Sant on October 21, 2019 per github request https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/475" ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "2A polypeptide region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "2A self-cleaving polypeptide region",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-10-21T10:41:49Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "2A_self_cleaving_peptide_region"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001374",
       "meta" : {
@@ -15405,16 +18232,17 @@
           "val" : "RNAMOD:087"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "five carboxymethyluridine",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "5-carboxymethyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "cm5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five carboxymethyluridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15425,52 +18253,101 @@
       "type" : "CLASS",
       "lbl" : "five_carboxymethyluridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000046",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001377",
       "meta" : {
         "definition" : {
-          "val" : "To insert a subsection of sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "3_methylpseudouridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+        "xrefs" : [ {
+          "val" : "RNAMOD:094"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "three methylpseudouridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3-methylpseudouridine",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m3Y",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert"
+      "lbl" : "three_methylpseudouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001377",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002221",
       "meta" : {
         "definition" : {
-          "val" : "3_methylpseudouridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A regulatory_region including the Transcription Start Site (TSS) of a gene and serving as a platform for Pre-Initiation Complex (PIC) assembly, enabling transcription of a gene under certain conditions.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:094"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m3Y",
+          "val" : "Eukaryotic promoter",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-07-31T14:01:20Z"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "three methylpseudouridine",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "eukaryotic_promoter"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000046",
+      "meta" : {
+        "definition" : {
+          "val" : "To insert a subsection of sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "insert"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002222",
+      "meta" : {
+        "definition" : {
+          "val" : "A regulatory_region essential for the specific initiation of transcription at a defined location in a DNA molecule, although this location might not be one single base. It is recognized by a specific RNA polymerase(RNAP)-holoenzyme, and this recognition is not necessarily autonomous.",
+          "xrefs" : [ "PMID:32665585" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3-methylpseudouridine",
+          "val" : "Prokaryotic promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-07-31T14:02:26Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_methylpseudouridine"
+      "lbl" : "prokaryotic_promoter"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001376",
       "meta" : {
@@ -15484,7 +18361,8 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "m5D",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "five methyldihydrouridine",
@@ -15509,12 +18387,10 @@
           "xrefs" : [ "SO:ke" ]
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "delete"
@@ -15530,15 +18406,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5-carboxymethylaminomethyl-2-thiouridine",
-          "xrefs" : [ ]
+          "val" : "cmnm5s2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "cmnm5s2U",
+          "val" : "five carboxymethylaminomethyl two thiouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five carboxymethylaminomethyl two thiouridine",
+          "val" : "5-carboxymethylaminomethyl-2-thiouridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15581,22 +18458,53 @@
           "pred" : "hasExactSynonym",
           "val" : "five carboxymethylaminomethyl two prime O methyluridine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5-carboxymethylaminomethyl- 2'-O-methyluridine",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "cmnm5Um",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "five_carboxymethylaminomethyl_two_prime_O_methyluridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002220",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant in which the function of a gene product is unknown with respect to a reference.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "function_uncertain_variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-carboxymethylaminomethyl- 2'-O-methyluridine",
+          "val" : "function uncertain variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-03-01T10:29:01Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_carboxymethylaminomethyl_two_prime_O_methyluridine"
+      "lbl" : "function_uncertain_variant"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001373",
       "meta" : {
@@ -15609,11 +18517,12 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine",
-          "xrefs" : [ ]
+          "val" : "m1acp3Y",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m1acp3Y",
+          "val" : "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15636,12 +18545,10 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "pseudogene_attribute"
@@ -15660,10 +18567,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "sequence_operation"
@@ -15680,7 +18585,8 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "m3U",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "three methyluridine",
@@ -15697,19 +18603,88 @@
       },
       "type" : "CLASS",
       "lbl" : "three_methyluridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002218",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant in which the function of a gene product is altered with respect to a reference.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "function modified variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "function_modified_variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "functionally abnormal",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-03-01T10:21:26Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "functionally_abnormal"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002219",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant in which the function of a gene product is retained with respect to a reference.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added after request from Lea Starita, lea.starita@gmail.com from the NCBI Feb 2019." ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "functionally normal",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "function retained variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "function_retained_variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-03-01T10:28:12Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "functionally_normal"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000037",
       "meta" : {
         "definition" : {
-          "val" : "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.",
+          "val" : "A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene.",
           "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "Definition updated Nov 10 2020, Colin Logie from GREEKC helped us realize that LCRs can also be located 3' to a gene." ],
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Locus_control_region"
         } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "locus control element",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -15717,15 +18692,15 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "locus control region",
+          "val" : "INSDC_qualifier:locus_control_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:locus_control_region",
+          "val" : "locus control region",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "pred" : "hasRelatedSynonym",
+          "val" : "locus control element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15747,7 +18722,7 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ncm5Um",
+          "val" : "five carbamoylmethyl two prime O methyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -15755,8 +18730,9 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five carbamoylmethyl two prime O methyluridine",
-          "xrefs" : [ ]
+          "val" : "ncm5Um",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -15765,6 +18741,62 @@
       },
       "type" : "CLASS",
       "lbl" : "five_carbamoylmethyl_two_prime_O_methyluridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002216",
+      "meta" : {
+        "definition" : {
+          "val" : "A promoter element with consensus sequence [5'-TCG(G/C)(A/T)xxTTxAA], bound by the transcription factor Pho7.",
+          "xrefs" : [ "PMID:28811350" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Pho7 binding site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-09-12T12:26:50Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "Pho7_binding_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001367",
+      "meta" : {
+        "definition" : {
+          "val" : "5_carbamoylmethyluridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:075"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "five carbamoylmethyluridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ncm5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5-carbamoylmethyluridine",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "five_carbamoylmethyluridine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000036",
       "meta" : {
@@ -15777,23 +18809,23 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "S/MAR",
+          "val" : "matrix attachment site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "MAR",
+          "val" : "INSDC_qualifier:matrix_attachment_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nuclear matrix association region",
+          "val" : "nuclear matrix attachment site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "matrix attachment site",
+          "val" : "S/MAR",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "scaffold attachment site",
+          "val" : "SMAR",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -15805,27 +18837,27 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:matrix_attachment_region",
+          "val" : "scaffold matrix attachment region",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "S/MAR element",
+          "pred" : "hasExactSynonym",
+          "val" : "MAR",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nuclear matrix attachment site",
+          "val" : "matrix association region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "SMAR",
+          "val" : "scaffold attachment site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "scaffold matrix attachment region",
+          "val" : "nuclear matrix association region",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "matrix association region",
+          "pred" : "hasRelatedSynonym",
+          "val" : "S/MAR element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15836,35 +18868,35 @@
       "type" : "CLASS",
       "lbl" : "matrix_attachment_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001367",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002217",
       "meta" : {
         "definition" : {
-          "val" : "5_carbamoylmethyluridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A sequence alteration which includes an insertion or a deletion. This describes a sequence length change when the direction of the change is unspecified or when such changes are pooled into one category.",
+          "xrefs" : [ "ZFIN:st" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:075"
-        } ],
+        "comments" : [ "This term is used when there is a change that is either an insertion or a deletion but it is unknown which event occurred." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ncm5U",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five carbamoylmethyluridine",
+          "val" : "unspecified indel",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-carbamoylmethyluridine",
+          "val" : "insertion or deletion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-02-24T18:26:05Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicoleruiz"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_carbamoylmethyluridine"
+      "lbl" : "unspecified_indel"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0002214",
       "meta" : {
@@ -15878,11 +18910,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-06-13T09:53:31Z"
@@ -15911,10 +18943,26 @@
       "type" : "CLASS",
       "lbl" : "match_part"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001369",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000038",
       "meta" : {
         "definition" : {
-          "val" : "5_carboxymethylaminomethyluridine is a modified uridine base feature.",
+          "val" : "A collection of match parts.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "match_set"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001369",
+      "meta" : {
+        "definition" : {
+          "val" : "5_carboxymethylaminomethyluridine is a modified uridine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
@@ -15922,15 +18970,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five carboxymethylaminomethyluridine",
-          "xrefs" : [ ]
+          "val" : "cmnm5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "5-carboxymethylaminomethyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "cmnm5U",
+          "val" : "five carboxymethylaminomethyluridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -15955,64 +19004,16 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-06-20T10:05:17Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "Zas1_recognition_motif"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000038",
-      "meta" : {
-        "definition" : {
-          "val" : "A collection of match parts.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "match_set"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001364",
-      "meta" : {
-        "definition" : {
-          "val" : "5_methylaminomethyluridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
-        },
-        "xrefs" : [ {
-          "val" : "RNAMOD:072"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "five methylaminomethyluridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mnm5U",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5-methylaminomethyluridine",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_methylaminomethyluridine"
+      "lbl" : "Zas1_recognition_motif"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0002212",
       "meta" : {
@@ -16026,14 +19027,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-04-18T11:14:04Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -16057,6 +19058,37 @@
       },
       "type" : "CLASS",
       "lbl" : "RNA_aptamer"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001364",
+      "meta" : {
+        "definition" : {
+          "val" : "5_methylaminomethyluridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:072"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "5-methylaminomethyluridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five methylaminomethyluridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mnm5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "five_methylaminomethyluridine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000032",
       "meta" : {
@@ -16085,46 +19117,46 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polyA site associated transcription termination signal",
+          "val" : "(A(U)GUA) motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Nrd1-dependent terminator",
+          "val" : "polyA site downstream element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "transcription termination signal",
+          "val" : "UCUUG motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polyA site downstream element",
+          "val" : "UGUAA/G motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Nrd1 binding motif",
+          "val" : "Nrd1-dependent terminator",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "(A(U)GUA) motif",
+          "val" : "Nrd1 binding motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "UCUUG motif",
+          "val" : "transcription termination signal",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "UGUAA/G motif",
+          "val" : "polyA site associated transcription termination signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-05-18T17:10:14Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -16141,15 +19173,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5-aminomethyl-2-thiouridine",
-          "xrefs" : [ ]
+          "val" : "nm5s2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "five aminomethyl two thiouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nm5s2U",
+          "val" : "5-aminomethyl-2-thiouridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16159,6 +19192,27 @@
       },
       "type" : "CLASS",
       "lbl" : "five_aminomethyl_two_thiouridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#contained_by",
+      "meta" : {
+        "definition" : {
+          "val" : "X contained_by Y iff X starts after start of Y and X ends before end of Y.",
+          "xrefs" : [ "PMID:20226267" ]
+        },
+        "comments" : [ "The inverse is contains. Example: intein contained_by immature_peptide_region." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T01:26:16Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "contained_by"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000035",
       "meta" : {
@@ -16170,10 +19224,6 @@
           "val" : "http://en.wikipedia.org/wiki/Riboswitch"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "riboswitch RNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasBroadSynonym",
           "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
@@ -16181,6 +19231,10 @@
           "pred" : "hasExactSynonym",
           "val" : "INSDC_qualifier:riboswitch",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "riboswitch RNA",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -16196,9 +19250,10 @@
           "val" : "A variation qualifying the presence of a sequence in a genome which is entirely missing in another genome.",
           "xrefs" : [ "BCS:bbean", "PMID:19956538", "PMID:25881062" ]
         },
+        "comments" : [ "Requested by Bayer Crop Science, March 2018" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "presence absence variation",
+          "val" : "PAV",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -16206,30 +19261,27 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "presence/absence_variation",
+          "val" : "presence absence variation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "presence-absence_variation",
+          "val" : "presence/absence variation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "PAV",
+          "val" : "presence/absence_variation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "presence/absence variation",
+          "val" : "presence-absence_variation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Crop Science, March 2018"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-03-21T12:59:14Z"
@@ -16249,12 +19301,13 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mnm5se2U",
+          "val" : "5-methylaminomethyl-2-selenouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-methylaminomethyl-2-selenouridine",
-          "xrefs" : [ ]
+          "val" : "mnm5se2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "five methylaminomethyl two selenouridine",
@@ -16267,29 +19320,6 @@
       },
       "type" : "CLASS",
       "lbl" : "five_methylaminomethyl_two_selenouridine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#contained_by",
-      "meta" : {
-        "definition" : {
-          "val" : "X contained_by Y iff X starts after start of Y and X ends before end of Y.",
-          "xrefs" : [ "PMID:20226267" ]
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T01:26:16Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The inverse is contains. Example: intein contained_by immature_peptide_region."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "contained_by"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0002211",
       "meta" : {
@@ -16316,23 +19346,27 @@
       "type" : "CLASS",
       "lbl" : "circular_plasmid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000034",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001365",
       "meta" : {
         "definition" : {
-          "val" : "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.",
-          "xrefs" : [ "http://www.gene-tools.com/" ]
+          "val" : "5_methylaminomethyl_2_thiouridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:073"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "morphant",
+          "pred" : "hasExactSynonym",
+          "val" : "5-methylaminomethyl-2-thiouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "morpholino oligo",
-          "xrefs" : [ ]
+          "val" : "mnm5s2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "morpholino",
+          "val" : "five methylaminomethyl two thiouridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16341,28 +19375,25 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "morpholino_oligo"
+      "lbl" : "five_methylaminomethyl_two_thiouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001365",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000034",
       "meta" : {
         "definition" : {
-          "val" : "5_methylaminomethyl_2_thiouridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino.",
+          "xrefs" : [ "http://www.gene-tools.com/" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:073"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mnm5s2U",
+          "val" : "morpholino",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five methylaminomethyl two thiouridine",
+          "pred" : "hasBroadSynonym",
+          "val" : "morphant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-methylaminomethyl-2-thiouridine",
+          "val" : "morpholino oligo",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16371,7 +19402,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_methylaminomethyl_two_thiouridine"
+      "lbl" : "morpholino_oligo"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001360",
       "meta" : {
@@ -16384,15 +19415,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mcm5U",
+          "val" : "five methoxycarbonylmethyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-methoxycarbonylmethyluridine",
-          "xrefs" : [ ]
+          "val" : "mcm5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five methoxycarbonylmethyluridine",
+          "val" : "5-methoxycarbonylmethyluridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16402,6 +19434,23 @@
       },
       "type" : "CLASS",
       "lbl" : "five_methoxycarbonylmethyluridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000031",
+      "meta" : {
+        "definition" : {
+          "val" : "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.",
+          "xrefs" : [ "http://aptamer.icmb.utexas.edu" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Aptamer"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "aptamer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001362",
       "meta" : {
@@ -16414,11 +19463,12 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five methoxycarbonylmethyl two thiouridine",
-          "xrefs" : [ ]
+          "val" : "mcm5s2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "mcm5s2U",
+          "val" : "five methoxycarbonylmethyl two thiouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -16432,23 +19482,6 @@
       },
       "type" : "CLASS",
       "lbl" : "five_methoxycarbonylmethyl_two_thiouridine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000031",
-      "meta" : {
-        "definition" : {
-          "val" : "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules.",
-          "xrefs" : [ "http://aptamer.icmb.utexas.edu" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Aptamer"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "aptamer"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001361",
       "meta" : {
@@ -16461,16 +19494,17 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five methoxycarbonylmethyl two prime O methyluridine",
+          "val" : "5-methoxycarbonylmethyl-2'-O-methyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "mcm5Um",
+          "val" : "five methoxycarbonylmethyl two prime O methyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-methoxycarbonylmethyl-2'-O-methyluridine",
-          "xrefs" : [ ]
+          "val" : "mcm5Um",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -16505,13 +19539,14 @@
           "val" : "A contig composed of genomic DNA derived sequences.",
           "xrefs" : [ "BCS:etrwz" ]
         },
+        "comments" : [ "Requested by Bayer Crop Science, March 2018" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gDNA contig",
+          "val" : "genomic DNA contig",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "genomic DNA contig",
+          "val" : "gDNA contig",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -16521,15 +19556,12 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-03-21T12:25:14Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Crop Science, March 2018"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
@@ -16547,11 +19579,11 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Watson-Crick pair",
+          "val" : "canonical base pair",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "canonical base pair",
+          "val" : "WC base pair",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
@@ -16559,7 +19591,7 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "WC base pair",
+          "val" : "Watson-Crick pair",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16582,11 +19614,11 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-02-06T12:23:24Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
@@ -16611,14 +19643,14 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-02-07T11:51:45Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -16630,6 +19662,7 @@
           "val" : "A regulatory element that acts in response to a stimulus, usually via transcription factor binding.",
           "xrefs" : [ ]
         },
+        "comments" : [ "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "INSDC_qualifier:response_element",
@@ -16644,18 +19677,49 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-10T16:33:25Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "response_element"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001357",
+      "meta" : {
+        "definition" : {
+          "val" : "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:065"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "uridine five oxyacetic acid methyl ester",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "uridine 5-oxyacetic acid methyl ester",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mcmo5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "response_element"
+      "lbl" : "uridine_five_oxyacetic_acid_methyl_ester"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000026",
       "meta" : {
@@ -16672,35 +19736,35 @@
       "type" : "CLASS",
       "lbl" : "RNA_junction_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001357",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002206",
       "meta" : {
         "definition" : {
-          "val" : "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Identifies the biological source of the specified span of the sequence",
+          "xrefs" : [ "NCBI:tm" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:065"
-        } ],
+        "comments" : [ "Terms such as genomic_DNA or mRNA can be used to describe a sequence source." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mcmo5U",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "uridine 5-oxyacetic acid methyl ester",
+          "val" : "INSDC_feature:source",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "uridine five oxyacetic acid methyl ester",
+          "val" : "sequence source",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-26T09:50:58Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "uridine_five_oxyacetic_acid_methyl_ester"
+      "lbl" : "sequence_source"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000025",
       "meta" : {
@@ -16732,15 +19796,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "uridine 5-oxyacetic acid",
-          "xrefs" : [ ]
+          "val" : "cmo5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "uridine five oxyacetic acid",
+          "val" : "uridine 5-oxyacetic acid",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "cmo5U",
+          "val" : "uridine five oxyacetic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16751,40 +19816,12 @@
       "type" : "CLASS",
       "lbl" : "uridine_five_oxyacetic_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002206",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000028",
       "meta" : {
         "definition" : {
-          "val" : "Identifies the biological source of the specified span of the sequence",
-          "xrefs" : [ "NCBI:tm" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:source",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence source",
+          "val" : "Two bases paired opposite each other by hydrogen bonds creating a secondary structure.",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-26T09:50:58Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Terms such as genomic_DNA or mRNA can be used to describe a sequence source."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "sequence_source"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000028",
-      "meta" : {
+        },
         "xrefs" : [ {
           "val" : "http://en.wikipedia.org/wiki/Base_pair"
         } ],
@@ -16808,10 +19845,6 @@
           "xrefs" : [ "NCBI:cf" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "replication start site",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasBroadSynonym",
           "val" : "INSDC_feature:misc_feature",
           "xrefs" : [ ]
@@ -16819,16 +19852,20 @@
           "pred" : "hasExactSynonym",
           "val" : "INSDC_note:replication_start_site",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "replication start site",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-09T11:23:35Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
@@ -16850,7 +19887,8 @@
         }, {
           "pred" : "hasExactSynonym",
           "val" : "mchm5U",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "5-(carboxyhydroxymethyl)uridine methyl ester",
@@ -16871,10 +19909,6 @@
           "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_feature",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "nucleotide cleavage site",
           "xrefs" : [ ]
@@ -16882,13 +19916,17 @@
           "pred" : "hasExactSynonym",
           "val" : "INSDC_note:nucleotide_cleavage_site",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_feature",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
           "val" : "2018-01-09T11:30:34Z"
@@ -16897,19 +19935,27 @@
       "type" : "CLASS",
       "lbl" : "nucleotide_cleavage_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000027",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001358",
       "meta" : {
+        "definition" : {
+          "val" : "5_carboxyhydroxymethyl_uridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:066"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "hook turn",
-          "xrefs" : [ ]
+          "pred" : "hasExactSynonym",
+          "val" : "chm5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "hook-turn motif",
+          "val" : "five carboxyhydroxymethyl uridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "RNA hook turn",
+          "val" : "5-(carboxyhydroxymethyl)uridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16918,28 +19964,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_hook_turn"
+      "lbl" : "five_carboxyhydroxymethyl_uridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001358",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000027",
       "meta" : {
-        "definition" : {
-          "val" : "5_carboxyhydroxymethyl_uridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
-        },
-        "xrefs" : [ {
-          "val" : "RNAMOD:066"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "five carboxyhydroxymethyl uridine",
+          "pred" : "hasRelatedSynonym",
+          "val" : "hook turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-(carboxyhydroxymethyl)uridine",
+          "val" : "hook-turn motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "chm5U",
+          "val" : "RNA hook turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16948,7 +19987,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_carboxyhydroxymethyl_uridine"
+      "lbl" : "RNA_hook_turn"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000066",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_by_polyadenylation_attribute"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001397",
       "meta" : {
@@ -16960,16 +20010,17 @@
           "val" : "MOD:00914"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "modified L phenylalanine",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
           "val" : "modified L-phenylalanine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "ModPhe",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "modified L phenylalanine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -16980,37 +20031,73 @@
       "type" : "CLASS",
       "lbl" : "modified_L_phenylalanine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000066",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002245",
       "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+        "definition" : {
+          "val" : "A partially_duplicated_transcript where the 5' end of the transcript is duplicated.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request from the Illumina group" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime duplicated transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5' duplicated transcript",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime partially duplicated transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T09:07:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_by_polyadenylation_attribute"
+      "lbl" : "five_prime_duplicated_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000065",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002246",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome structure variation whereby an arm exists as an individual chromosome element.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A partially_duplicated_transcript where the 3' end of the transcript is duplicated.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from the Illumina group" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "free chromosome arm",
+          "val" : "3' duplicated transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "three prime partially duplicated transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "three prime duplicated transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T09:07:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "free_chromosome_arm"
+      "lbl" : "three_prime_duplicated_transcript"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001396",
       "meta" : {
@@ -17023,12 +20110,13 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ModIle",
+          "val" : "modified L-isoleucine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-isoleucine",
-          "xrefs" : [ ]
+          "val" : "ModIle",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "modified L isoleucine",
@@ -17042,19 +20130,24 @@
       "type" : "CLASS",
       "lbl" : "modified_L_isoleucine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000068",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000065",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a gene that has a sequence that overlaps the sequence of another gene.",
+          "val" : "A chromosome structure variation whereby an arm exists as an individual chromosome element.",
           "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "free chromosome arm",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "overlapping"
+      "lbl" : "free_chromosome_arm"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001399",
       "meta" : {
@@ -17067,15 +20160,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "MosSer",
+          "val" : "modified L-serine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L serine",
-          "xrefs" : [ ]
+          "val" : "MosSer",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-serine",
+          "val" : "modified L serine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -17086,35 +20180,49 @@
       "type" : "CLASS",
       "lbl" : "modified_L_serine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001398",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002243",
       "meta" : {
         "definition" : {
-          "val" : "A post translationally modified histidine amino acid feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene which codes for 23S_rRNA, which functions as a component of the large subunit of the ribosome in prokaryotes.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "MOD:00909"
-        } ],
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L histidine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "modified L-histidine",
+          "val" : "23S_rRNA_gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModHis",
+          "val" : "23S rRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_L_histidine"
+      "lbl" : "cytosolic_rRNA_23S_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000068",
+      "meta" : {
+        "definition" : {
+          "val" : "An attribute describing a gene that has a sequence that overlaps the sequence of another gene.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "overlapping"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000067",
       "meta" : {
@@ -17131,26 +20239,52 @@
       "type" : "CLASS",
       "lbl" : "gene_to_gene_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001393",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002244",
       "meta" : {
         "definition" : {
-          "val" : "A post translationally modified tryptophan amino acid feature.",
+          "val" : "A transcript which is partially duplicated due to duplication of DNA, leading to a new transcript that is only partial and likely nonfunctional.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request from the Illumina group" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "partially duplicated transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T09:07:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "partially_duplicated_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001398",
+      "meta" : {
+        "definition" : {
+          "val" : "A post translationally modified histidine amino acid feature.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "MOD:00918"
+          "val" : "MOD:00909"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-tryptophan",
+          "val" : "ModHis",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModTrp",
+          "val" : "modified L histidine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L tryptophan",
+          "val" : "modified L-histidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -17159,7 +20293,7 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_L_tryptophan"
+      "lbl" : "modified_L_histidine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000062",
       "meta" : {
@@ -17180,31 +20314,70 @@
       "type" : "CLASS",
       "lbl" : "deficient_intrachromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000061",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001393",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A post translationally modified tryptophan amino acid feature.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "MOD:00918"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "restriction enzyme binding site",
+          "val" : "modified L tryptophan",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "restriction endonuclease binding site",
+          "val" : "ModTrp",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "modified L-tryptophan",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A region of a molecule that binds to a restriction enzyme."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_binding_site"
+      "lbl" : "modified_L_tryptophan"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002241",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene which codes for 21S_rRNA, which functions as a component of the large subunit of the ribosome in mitochondria.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472) Removed relationship derives_from SO:0001171 on 10 June 2021 when SO:0001171 rRNA_21S was obsoleted into SO:0002345 mt_LSU_rRNA. See GitHub Issue #493. OBSOLETED on 12 September 2022, merged into SO:0002364 mt_LSU_rRNA_gene see GitHub Issue #513." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "21S rRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "21S_rRNA_gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0002364"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "rRNA_21S_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001392",
       "meta" : {
@@ -17217,15 +20390,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-threonine",
-          "xrefs" : [ ]
+          "val" : "ModThr",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "modified L threonine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModThr",
+          "val" : "modified L-threonine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -17235,6 +20409,60 @@
       },
       "type" : "CLASS",
       "lbl" : "modified_L_threonine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002242",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene which codes for 25S_rRNA, which functions as a component of the large subunit of the ribosome in some eukaryotes.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "25S_rRNA_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "25S rRNA gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cytosolic_rRNA_25S_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000061",
+      "meta" : {
+        "definition" : {
+          "val" : "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme.",
+          "xrefs" : [ "SO:cb" ]
+        },
+        "comments" : [ "A region of a molecule that binds to a restriction enzyme." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "restriction endonuclease binding site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "restriction enzyme binding site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "restriction_enzyme_binding_site"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001395",
       "meta" : {
@@ -17247,12 +20475,13 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ModMet",
+          "val" : "modified L methionine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L methionine",
-          "xrefs" : [ ]
+          "val" : "ModMet",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "modified L-methionine",
@@ -17268,49 +20497,49 @@
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000064",
       "meta" : {
+        "comments" : [ "This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "gene_by_transcript_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001394",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002240",
       "meta" : {
         "definition" : {
-          "val" : "A post translationally modified glutamine amino acid feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene which codes for 5_8S_rRNA (5.8S rRNA), which functions as a component of the large subunit of the ribosome in eukaryotes.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "MOD:00907"
-        } ],
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified L glutamine",
+          "val" : "5_8S rRNA gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-glutamine",
+          "val" : "5_8S_rRNA_gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModGln",
+          "val" : "5.8S rRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_L_glutamine"
+      "lbl" : "cytosolic_rRNA_5_8S_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000063",
       "meta" : {
@@ -17331,26 +20560,42 @@
       "type" : "CLASS",
       "lbl" : "deficient_interchromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000060",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001394",
       "meta" : {
+        "definition" : {
+          "val" : "A post translationally modified glutamine amino acid feature.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "MOD:00907"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "compound chromosome arm",
+          "val" : "modified L-glutamine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "modified L glutamine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ModGln",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "FLAG - this term is should probably be a part of rather than an is_a."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "compound_chromosome_arm"
+      "lbl" : "modified_L_glutamine"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001391",
       "meta" : {
+        "definition" : {
+          "val" : "A post translationally modified glutamic acid.",
+          "xrefs" : [ ]
+        },
         "xrefs" : [ {
           "val" : "MOD:00906"
         } ],
@@ -17360,12 +20605,13 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModGlu",
+          "val" : "modified L-glutamic acid",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-glutamic acid",
-          "xrefs" : [ ]
+          "val" : "ModGlu",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -17374,6 +20620,26 @@
       },
       "type" : "CLASS",
       "lbl" : "modified_L_glutamic_acid"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000060",
+      "meta" : {
+        "definition" : {
+          "val" : "One arm of a compound chromosome.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "FLAG - this term is should probably be a part of rather than an is_a." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "compound chromosome arm",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "compound_chromosome_arm"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001390",
       "meta" : {
@@ -17390,12 +20656,13 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModCys",
+          "val" : "modified L cysteine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L cysteine",
-          "xrefs" : [ ]
+          "val" : "ModCys",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -17425,45 +20692,88 @@
       "type" : "CLASS",
       "lbl" : "nuclease_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000058",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002238",
       "meta" : {
+        "definition" : {
+          "val" : "A gene which codes for 5S_rRNA, which is a portion of the large subunit of the ribosome in both eukaryotes and prokaryotes.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "assortment-derived_aneuploid",
+          "pred" : "hasExactSynonym",
+          "val" : "5S rRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5S_rRNA_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "assortment_derived_aneuploid"
+      "lbl" : "cytosolic_rRNA_5S_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001389",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002239",
       "meta" : {
         "definition" : {
-          "val" : "A post translationally modified aspartic acid amino acid feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene which codes for 28S_rRNA, which functions as a component of the large subunit of the ribosome in eukaryotes.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "MOD:00904"
-        } ],
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ModAsp",
+          "val" : "28S rRNA gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L-aspartic acid",
+          "val" : "28S_rRNA_gene",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cytosolic_rRNA_28S_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001389",
+      "meta" : {
+        "definition" : {
+          "val" : "A post translationally modified aspartic acid amino acid feature.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "MOD:00904"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
           "val" : "modified L aspartic acid",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "modified L-aspartic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ModAsp",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -17473,22 +20783,81 @@
       "type" : "CLASS",
       "lbl" : "modified_L_aspartic_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000055",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000058",
+      "meta" : {
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "assortment-derived_aneuploid",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "assortment_derived_aneuploid"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002236",
       "meta" : {
         "definition" : {
-          "val" : "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene which codes for 18S_rRNA, which functions as the small subunit of the ribosome in eukaryotes.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Hyperploid"
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "18S_rRNA_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "18S rRNA gene",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "hyperploid"
+      "lbl" : "cytosolic_rRNA_18S_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002237",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene which codes for 16S_rRNA, which functions as the small subunit of the ribosome in prokaryotes.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request by Antonia Lock GitHub issue #472 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/472). Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "16S rRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "16S_rRNA_gene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-07T16:12:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cytosolic_rRNA_16S_gene"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001386",
       "meta" : {
@@ -17500,21 +20869,107 @@
           "val" : "MOD:00908"
         } ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "modified glycine",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
           "val" : "ModGly",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "modified_glycine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000055",
+      "meta" : {
+        "definition" : {
+          "val" : "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Hyperploid"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "hyperploid"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002234",
+      "meta" : {
+        "definition" : {
+          "val" : "A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA).",
+          "xrefs" : [ "PMID:30601114" ]
+        },
+        "comments" : [ "Added as per request by Val Wood GitHub issue #455 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/455)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "pumilio response element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified glycine",
+          "val" : "PRE binding RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-04-14T10:40:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_glycine"
+      "lbl" : "pumilio_response_element"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002235",
+      "meta" : {
+        "definition" : {
+          "val" : "A polypeptide region that mediates binding to SUMO. The motif contains a hydrophobic core sequence consisting of three or four Ile, Leu, or Val residues plus one acidic or polar residue at position 2 or 3.",
+          "xrefs" : [ "PMID:15388847,PMID:16524884" ]
+        },
+        "comments" : [ "Added as per request GitHub issue #434 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/434)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "SUMO interaction motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "SIM",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "SBM",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "SUMO binding motif",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-04-22T12:40:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "SUMO_interaction_motif"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001385",
       "meta" : {
@@ -17551,6 +21006,30 @@
       },
       "type" : "CLASS",
       "lbl" : "aneuploid"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000057",
+      "meta" : {
+        "definition" : {
+          "val" : "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Operator_(biology)#Operator"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "operator segment",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "operator"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001388",
       "meta" : {
@@ -17563,7 +21042,7 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ModAsn",
+          "val" : "modified L asparagine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
@@ -17571,8 +21050,9 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L asparagine",
-          "xrefs" : [ ]
+          "val" : "ModAsn",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -17582,28 +21062,82 @@
       "type" : "CLASS",
       "lbl" : "modified_L_asparagine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000057",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002232",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A genetic feature that encodes a trait used for artificial selection of a subpopulation.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Operator_(biology)#Operator"
+        "comments" : [ "Added as per request by Bryan Bartley GitHub issue #468 and #402 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/468)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "selection marker",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "selectable_marker",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "selectable marker",
+          "xrefs" : [ ]
         } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-04-01T10:04:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "selection_marker"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002233",
+      "meta" : {
+        "definition" : {
+          "val" : "A chromosomal locus where complementary lncRNA and associated proteins accumulate at the corresponding lncRNA gene loci to tether homologous chromosome during chromosome pairing at meiosis I.",
+          "xrefs" : [ "PMID:22582262", "PMID:31811152" ]
+        },
+        "comments" : [ "Added as per request by Val Wood GitHub issue #483 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/483)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "operator segment",
+          "val" : "homologous chromosome recognition and pairing locus",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-04-14T10:09:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "operator"
+      "lbl" : "homologous_chromosome_recognition_and_pairing_locus"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000056",
+      "meta" : {
+        "definition" : {
+          "val" : "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Hypoploid"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "hypoploid"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001387",
       "meta" : {
@@ -17620,12 +21154,13 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ModAla",
+          "val" : "modified L alanine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified L alanine",
-          "xrefs" : [ ]
+          "val" : "ModAla",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#AAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -17635,26 +21170,35 @@
       "type" : "CLASS",
       "lbl" : "modified_L_alanine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000056",
+      "id" : "http://purl.obolibrary.org/obo/IAO_0100001",
+      "type" : "PROPERTY",
+      "lbl" : "term replaced by"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002230",
       "meta" : {
         "definition" : {
-          "val" : "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A C-terminus protein motif (CAAX) serving as a post-translational prenylation site modified by the attachment of either a farnesyl or a geranyl-geranyl group to a cysteine residue. Farnesyltransferase recognizes CaaX boxes where X = M, S, Q, A, or C, whereas Geranylgeranyltransferase I recognizes CaaX boxes with X = L or E.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Hypoploid"
+        "comments" : [ "Added as per request by Val Wood GitHub issue #479 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/479)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "CAAX box",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-03-27T18:04:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "hypoploid"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/IAO_0100001",
-      "type" : "PROPERTY",
-      "lbl" : "term replaced by"
+      "lbl" : "CAAX_box"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001382",
       "meta" : {
@@ -17667,12 +21211,13 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inm5Um",
+          "val" : "five isopentenylaminomethyl two prime O methyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five isopentenylaminomethyl two prime O methyluridine",
-          "xrefs" : [ ]
+          "val" : "inm5Um",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "5-(isopentenylaminomethyl)- 2'-O-methyluridine",
@@ -17714,15 +21259,16 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five isopentenylaminomethyl two thiouridine",
-          "xrefs" : [ ]
+          "val" : "inm5s2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "inm5s2U",
+          "val" : "5-(isopentenylaminomethyl)- 2-thiouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-(isopentenylaminomethyl)- 2-thiouridine",
+          "val" : "five isopentenylaminomethyl two thiouridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -17732,6 +21278,32 @@
       },
       "type" : "CLASS",
       "lbl" : "five_isopentenylaminomethyl_two_thiouridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002231",
+      "meta" : {
+        "definition" : {
+          "val" : "An RNA that catalyzes its own cleavage.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request by John T. Sexton GitHub issue #470 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/470)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "self cleaving ribozyme",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-03-30T16:02:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "self_cleaving_ribozyme"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000050",
       "meta" : {
@@ -17743,23 +21315,25 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "gene_part"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001384",
       "meta" : {
+        "definition" : {
+          "val" : "A portion of a CDS that is not the complete CDS.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "incomplete CDS",
+          "val" : "CDS fragment",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "CDS fragment",
+          "val" : "incomplete CDS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -17776,6 +21350,7 @@
           "val" : "A sequence_variant_effect which changes the regulatory region of a gene.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
           "val" : "mutation affecting regulatory region",
@@ -17786,18 +21361,13 @@
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "SO:0001556"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "sequence_variant_affecting_regulatory_region"
@@ -17831,10 +21401,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "assortment_derived_deficiency"
@@ -17850,16 +21418,17 @@
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five isopentenylaminomethyl uridine",
+          "val" : "5-(isopentenylaminomethyl)uridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-(isopentenylaminomethyl)uridine",
+          "val" : "five isopentenylaminomethyl uridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
           "val" : "inm5U",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -17868,6 +21437,93 @@
       },
       "type" : "CLASS",
       "lbl" : "five_isopentenylaminomethyl_uridine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002229",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant extending the CDS at the 3' end, that causes elongation of the resulting polypeptide sequence at the C terminus.",
+          "xrefs" : [ "PMID:14732127", "PMID:15864293", "PMID:27984720", "PMID:31216041", "PMID:32020195" ]
+        },
+        "comments" : [ "Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "elongated CDS three prime",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "elongated_CDS_three_prime",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CDS Extension three prime",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CDS Extension 3 prime",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-03-27T17:58:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "CDS_three_prime_extension"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002227",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant extending the CDS, that causes elongation of the resulting polypeptide sequence.",
+          "xrefs" : [ "PMID:14732127", "PMID:15864293", "PMID:27984720", "PMID:31216041", "PMID:32020195" ]
+        },
+        "comments" : [ "Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "CDS Extension",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "elongated_CDS",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "elongated CDS",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-03-27T17:56:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "CDS_extension"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000048",
+      "meta" : {
+        "definition" : {
+          "val" : "To substitute a subsection of sequence for another.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "substitute"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0001379",
       "meta" : {
@@ -17881,7 +21537,8 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "tm5s2U",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
           "val" : "five taurinomethyl two thiouridine",
@@ -17899,22 +21556,43 @@
       "type" : "CLASS",
       "lbl" : "five_taurinomethyl_two_thiouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000048",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002228",
       "meta" : {
         "definition" : {
-          "val" : "To substitute a subsection of sequence for another.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence variant extending the CDS at the 5' end, that causes elongation of the resulting polypeptide sequence at the N terminus.",
+          "xrefs" : [ "PMID:14732127", "PMID:15864293", "PMID:27984720", "PMID:31216041", "PMID:32020195" ]
         },
+        "comments" : [ "Added as per request by Edward Wallace GitHub issue #480 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/480)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "elongated CDS five prime",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CDS Extension 5 prime",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CDS Extension five prime",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "elongated_CDS_five_prime",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-03-27T17:57:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "substitute"
+      "lbl" : "CDS_five_prime_extension"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000047",
       "meta" : {
@@ -17925,10 +21603,8 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "invert"
@@ -17945,14 +21621,15 @@
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
           "val" : "tm5U",
-          "xrefs" : [ ]
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-taurinomethyluridine",
+          "val" : "five taurinomethyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five taurinomethyluridine",
+          "val" : "5-taurinomethyluridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -17966,6 +21643,40 @@
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
       "type" : "PROPERTY",
       "lbl" : "has_alternative_id"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002225",
+      "meta" : {
+        "definition" : {
+          "val" : "A conserved sequence (5'-CGNMGATCNTY-3') transcription repressor binding site required for gene repression in the presence of high zinc.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added on October 30, 2019 as per request of Val Wood request on GitHub Issue# 476 https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/476" ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "LRE element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "LRE",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "Loz1 response element",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2019-10-30T11:19:52Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "LOZ1_response_element"
     }, {
       "id" : "http://purl.obolibrary.org/obo/SO_0000049",
       "meta" : {
@@ -17976,71 +21687,83 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "translocate"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000088",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002226",
       "meta" : {
         "definition" : {
-          "val" : "A gene located in mitochondrial sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A group II intron that recognizes IBS1/EBS1 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon and may also recognize a stem-loop in the RNA.",
+          "xrefs" : [ "PMID:20463000" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Mitochondrial_gene"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mt gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mitochondrial gene",
+          "val" : "group IIB intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-03-27T08:56:34Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mt_gene"
+      "lbl" : "group_IIC_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000087",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002267",
       "meta" : {
         "definition" : {
-          "val" : "A gene from nuclear sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein.",
+          "xrefs" : [ "PMID:17984973" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Nuclear_gene"
-        } ],
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nuclear gene",
+          "val" : "RLR retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Retrovirus LTR retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclear_gene"
+      "lbl" : "Retrovirus_LTR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000089",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000088",
       "meta" : {
         "definition" : {
-          "val" : "A gene located in kinetoplast sequence.",
+          "val" : "A gene located in mitochondrial sequence.",
           "xrefs" : [ "SO:xp" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Mitochondrial_gene"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "kinetoplast gene",
+          "val" : "mt gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mitochondrial gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18049,28 +21772,54 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "kinetoplast_gene"
+      "lbl" : "mt_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000084",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002268",
       "meta" : {
+        "definition" : {
+          "val" : "Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses (Type D). F-Class III families are similar to foamy viruses.",
+          "xrefs" : [ "PMID:17984973" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "micronuclear sequence",
+          "val" : "HERV",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RLE retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Endogenous Retrovirus LTR retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "micronuclear_sequence"
+      "lbl" : "Endogenous_Retrovirus_LTR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000083",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000087",
       "meta" : {
+        "definition" : {
+          "val" : "A gene from nuclear sequence.",
+          "xrefs" : [ "SO:xp" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Nuclear_gene"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "macronuclear sequence",
+          "val" : "nuclear gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18079,85 +21828,86 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "macronuclear_sequence"
+      "lbl" : "nuclear_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000086",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002265",
       "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+        "definition" : {
+          "val" : "LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.",
+          "xrefs" : [ "PMID:17984973" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "RLG retrotransposon",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "gene_by_organelle_of_genome"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000085",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "hasExactSynonym",
+          "val" : "Ty3 retrotransposon",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "gene_by_genome_location"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000080",
-      "meta" : {
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "operon member",
+          "val" : "Gypsy LTR retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "operon_member"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000082",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "processed_transcript_attribute"
+      "lbl" : "Gypsy_LTR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000081",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002266",
       "meta" : {
+        "definition" : {
+          "val" : "LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.",
+          "xrefs" : [ "PMID:17984973" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene array member",
+          "val" : "Bel Pao LTR retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Bel-Pao LTR retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RLB retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_array_member"
+      "lbl" : "Bel_Pao_LTR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000077",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000089",
       "meta" : {
         "definition" : {
-          "val" : "A region sequence that is complementary to a sequence of messenger RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene located in kinetoplast sequence.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Antisense"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "kinetoplast gene",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -18165,21 +21915,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "antisense"
+      "lbl" : "kinetoplast_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000076",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000084",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA belonging to the micronuclei of a cell.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5' 3' overlap",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "three prime five prime overlap",
+          "val" : "micronuclear sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18188,36 +21934,55 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_five_prime_overlap"
+      "lbl" : "micronuclear_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000079",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002263",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that is dicistronic.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An absolute reference to the strand. When a chromosome has p and q arms, the Crick strand is the strand whose 5'-end is on the long arm of the chromosome. Of note, the term 'minus strand' is typically based on a reference sequence where it's preferred for the minus strand to be the Crick strand, but might not be and 'minus strand' is therefore not an exact synonym.",
+          "xrefs" : [ "PMID:21303550" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419)" ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "Minus strand",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "dicistronic transcript",
+          "val" : "Crick strand",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Reverse strand",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Bottom strand",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-28T10:33:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dicistronic_transcript"
+      "lbl" : "Crick_strand"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000078",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000083",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that is polycistronic.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "DNA belonging to the macronuclei of ciliates.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polycistronic transcript",
+          "val" : "macronuclear sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18226,106 +21991,141 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polycistronic_transcript"
+      "lbl" : "macronuclear_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000073",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002264",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H.",
+          "xrefs" : [ "PMID:17984973" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime-three prime overlap",
+          "val" : "RLC retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ty1 retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Copia LTR retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_three_prime_overlap"
+      "lbl" : "Copia_LTR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000072",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000086",
       "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "end_overlapping_gene"
+      "lbl" : "gene_by_organelle_of_genome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000075",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002261",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "TRIM elements have terminal direct repeat sequences of 100-250 bp in length that flank an internal domain of 100–300 bp. TRIMs lack coding domains and thus do not encode proteins.",
+          "xrefs" : [ "PMID:11717436" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime-three prime overlap",
+          "val" : "terminal-repeat retrotransposons in miniature",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "terminal-repeat_retrotransposons_in_miniature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-27T15:47:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_three_prime_overlap"
+      "lbl" : "TRIM"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000074",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000085",
       "meta" : {
-        "definition" : {
-          "val" : "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "five prime-five prime overlap",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_five_prime_overlap"
+      "lbl" : "gene_by_genome_location"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000071",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002262",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a gene when it is located within the intron of another gene and on the same strand.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An absolute reference to the strand. When a chromosome has p and q arms, the Watson strand is the strand whose 5'-end is on the short arm of the chromosome. Of note, the term 'plus strand' is typically based on a reference sequence where it's preferred for the plus strand to be the Watson strand, but might not be and 'plus strand' is therefore not an exact synonym.",
+          "xrefs" : [ "PMID:21303550" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #419 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/419)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inside intron parallel",
+          "val" : "Watson strand",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Top strand",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "Plus strand",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Forward strand",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-28T10:33:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inside_intron_parallel"
+      "lbl" : "Watson_strand"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000070",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000080",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that is a member of an operon, which is a set of genes transcribed together as a unit.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inside intron antiparallel",
+          "val" : "operon member",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18334,122 +22134,162 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inside_intron_antiparallel"
+      "lbl" : "operon_member"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000069",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002260",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a gene when it is located within the intron of another gene.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Large Retrotransposon Derivative elements are long-terminal repeats that contain reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins . The LARDs identified in barley and other Triticeae have LTRs ~5.5 kb and an interal domain of ~3.5 kb. LARDs lack coding domains and thus do not encode proteins.",
+          "xrefs" : [ "PMID:15082561" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #429 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/429)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inside intron",
+          "val" : "Large Retrotransposon Derivative",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "large_retrotransposon_derivative",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-27T15:47:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inside_intron"
+      "lbl" : "LARD"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#evidence_for_feature",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000082",
       "meta" : {
-        "definition" : {
-          "val" : "B is evidence_for_feature A, if an instance of B supports the existence of A.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222."
-        } ]
+        } ],
+        "deprecated" : true
       },
-      "type" : "PROPERTY",
-      "lbl" : "evidence_for_feature"
+      "type" : "CLASS",
+      "lbl" : "processed_transcript_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#derives_from",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000081",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "gene array member",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "derives_from"
+      "type" : "CLASS",
+      "lbl" : "gene_array_member"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000099",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002258",
       "meta" : {
         "definition" : {
-          "val" : "A gene from proviral sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A binding motif with the consensus sequence TTAGGG to which Teb1 binds.",
+          "xrefs" : [ "PMID:23314747", "PMID:27901072" ]
         },
+        "comments" : [ "Requested by Antonia Locke, (Pombe) as per GitHub Issue Request #439 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/439)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "proviral gene",
+          "val" : "teb1 recognition motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-27T11:03:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "proviral_gene"
+      "lbl" : "teb1_recognition_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000098",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002259",
       "meta" : {
         "definition" : {
-          "val" : "A gene from plasmid sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A region defined by a cluster of experimentally determined polyadenylation sites, typically less than 25 bp in length and associated with a single polyadenylation signal.",
+          "xrefs" : [ "PMID:17202160", "PMID:24072873", "PMID:25906188" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #450 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/450)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plasmid gene",
+          "val" : "polyA_cluster",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "polyA cluster",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "polyA site cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-27T14:17:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plasmid_gene"
+      "lbl" : "polyA_site_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000095",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002256",
       "meta" : {
         "definition" : {
-          "val" : "A plastid gene from leucoplast sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A region of a stem in a stem loop structure where the sequences are non-complimentary.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "leucoplast gene",
+          "val" : "non-complimentary stem",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "noncomplimentary stem",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T11:40:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "leucoplast_gene"
+      "lbl" : "non_complimentary_stem"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000094",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000077",
       "meta" : {
         "definition" : {
-          "val" : "A gene from cyanelle sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A region sequence that is complementary to a sequence of messenger RNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "cyanelle gene",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Antisense"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -18457,36 +22297,47 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cyanelle_gene"
+      "lbl" : "antisense"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000097",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002257",
       "meta" : {
         "definition" : {
-          "val" : "A gene from nucleomorph sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "Cytologically observable heterochromatic regions of chromosomes away from centromeres that contain predominatly large tandem repeats and retrotransposons.",
+          "xrefs" : [ "PMID:6439888" ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #487 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/487)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nucleomorph gene",
+          "val" : "Heterochromatin Knob",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-27T10:45:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nucleomorph_gene"
+      "lbl" : "knob"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000096",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000076",
       "meta" : {
         "definition" : {
-          "val" : "A gene from proplastid sequence.",
+          "val" : "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "proplastid gene",
+          "val" : "5' 3' overlap",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "three prime five prime overlap",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18495,36 +22346,43 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "proplastid_gene"
+      "lbl" : "three_prime_five_prime_overlap"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000091",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002254",
       "meta" : {
         "definition" : {
-          "val" : "A gene from apicoplast sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "The loop portion of a stem loop, which is not folded back upon itself. ",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "apicoplast gene",
+          "val" : "loop portion of stem loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T11:40:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "apicoplast_gene"
+      "lbl" : "loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000090",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000079",
       "meta" : {
         "definition" : {
-          "val" : "A gene from plastid sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A transcript that is dicistronic.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plastid gene",
+          "val" : "dicistronic transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18533,40 +22391,43 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plastid_gene"
+      "lbl" : "dicistronic_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000093",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002255",
       "meta" : {
         "definition" : {
-          "val" : "A gene from chromoplast_sequence.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "The portion of a stem loop where the RNA is folded back upon itself. ",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromoplast gene",
+          "val" : "stem portion of stem loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T11:40:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromoplast_gene"
+      "lbl" : "stem"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000092",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000078",
       "meta" : {
         "definition" : {
-          "val" : "A gene from chloroplast sequence.",
+          "val" : "A transcript that is polycistronic.",
           "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ct gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "chloroplast gene",
+          "val" : "polycistronic transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -18575,618 +22436,754 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ct_gene"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#dbvar",
-      "type" : "PROPERTY",
-      "lbl" : "DBVAR"
+      "lbl" : "polycistronic_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#has_part",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000073",
       "meta" : {
         "definition" : {
-          "val" : "Inverse of part_of.",
-          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
+          "val" : "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime-three prime overlap",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: operon has_part gene."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "has_part"
+      "type" : "CLASS",
+      "lbl" : "five_prime_three_prime_overlap"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000092",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002252",
       "meta" : {
         "definition" : {
-          "val" : "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "CDS region corresponding to a transit peptide region of a polypeptide.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing complex change of translational product",
+          "val" : "INSDC_feature:transit_peptide",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing complex change of translational product",
+          "pred" : "hasExactSynonym",
+          "val" : "transit peptide region of CDS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001539"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T13:40:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_complex_change_of_translational_product"
+      "lbl" : "transit_peptide_region_of_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000096",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002253",
       "meta" : {
         "definition" : {
-          "val" : "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A portion of a stem loop secondary structure in RNA.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #451 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/451)" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing amino acid insertion",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing amino acid insertion",
+          "val" : "stem loop region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T11:40:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001605"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_amino_acid_insertion"
+      "lbl" : "stem_loop_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000095",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000072",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing nonconservative amino acid substitution",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing nonconservative amino acid substitution",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001607"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_nonconservative_amino_acid_substitution"
+      "lbl" : "end_overlapping_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000094",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002250",
       "meta" : {
+        "definition" : {
+          "val" : "A CDS region corresponding to a propeptide of a polypeptide.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing conservative amino acid substitution",
+          "pred" : "hasExactSynonym",
+          "val" : "propeptide region of CDS",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing conservative amino acid substitution",
+          "val" : "INSDC_feature:propeptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001607"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T13:40:30Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_conservative_amino_acid_substitution"
+      "lbl" : "propeptide_region_of_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000093",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000075",
       "meta" : {
         "definition" : {
-          "val" : "The replacement of a single amino acid by another.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing amino acid substitution",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing amino acid substitution",
+          "val" : "three prime-three prime overlap",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001606"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_amino_acid_substitution"
+      "lbl" : "three_prime_three_prime_overlap"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000099",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000074",
       "meta" : {
         "definition" : {
-          "val" : "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing polypeptide elongation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing polypeptide elongation",
+          "val" : "five prime-five prime overlap",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001609"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_polypeptide_elongation"
+      "lbl" : "five_prime_five_prime_overlap"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000098",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002251",
       "meta" : {
         "definition" : {
-          "val" : "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062).",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A CDS region corresponding to a signal peptide of a polypeptide.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing polypeptide truncation",
+          "val" : "INSDC_feature:sig_peptide",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing polypeptide truncation",
+          "pred" : "hasExactSynonym",
+          "val" : "Signal peptide region of CDS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001587"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T13:40:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_polypeptide_truncation"
+      "lbl" : "signal_peptide_region_of_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000097",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000071",
       "meta" : {
         "definition" : {
-          "val" : "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An attribute to describe a gene when it is located within the intron of another gene and on the same strand.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing amino acid deletion",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing amino acid deletion",
+          "val" : "inside intron parallel",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001825"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_amino_acid_deletion"
+      "lbl" : "inside_intron_parallel"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000918",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000070",
       "meta" : {
         "definition" : {
-          "val" : "An edit to delete a uridine.",
+          "val" : "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "delete U",
+          "val" : "inside intron antiparallel",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "delete_U"
+      "lbl" : "inside_intron_antiparallel"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000917",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002249",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a U.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A CDS region corresponding to a mature protein region of a polypeptide.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #484 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/484)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert U",
+          "val" : "mature protein region of CDS",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:mat_peptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T13:40:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_U"
+      "lbl" : "mature_protein_region_of_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000919",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000069",
       "meta" : {
         "definition" : {
-          "val" : "An edit to substitute an I for an A.",
+          "val" : "An attribute to describe a gene when it is located within the intron of another gene.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "substitute A to I",
+          "val" : "inside intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "substitute_A_to_I"
+      "lbl" : "inside_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000914",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002247",
       "meta" : {
         "definition" : {
-          "val" : "A clone insert made from genomic DNA.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A non-coding RNA less than 200 nucleotides in length.",
+          "xrefs" : [ "PMID:30069443" ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cloned genomic insert",
+          "val" : "Small noncoding RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T11:07:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cloned_genomic_insert"
+      "lbl" : "sncRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000913",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002248",
       "meta" : {
         "definition" : {
-          "val" : "A clone insert made from cDNA.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A region of DNA that is predicted to be translated and transcribed into a protein by a protein detection algorithm that does not get transcribed in nature.",
+          "xrefs" : [ "PMID:21771858" ]
         },
+        "comments" : [ "Added as per request from GitHub Issue #478 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/478)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cloned cDNA insert",
+          "val" : "spurious protein",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-05-13T11:40:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cloned_cDNA_insert"
+      "lbl" : "spurious_protein"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000916",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002289",
       "meta" : {
+        "definition" : {
+          "val" : "VIPER retrotransposons are members of the YR_retrotransposon (SO:0002286 superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes.",
+          "xrefs" : [ "PMID:16297462" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "edit operation",
+          "val" : "Viper retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RYV retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Viper YR retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edit_operation"
+      "lbl" : "Viper_YR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000915",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002287",
       "meta" : {
         "definition" : {
-          "val" : "A clone insert that is engineered.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase.",
+          "xrefs" : [ "PMID:24086727" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered insert",
+          "val" : "DIRS YR retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RYD retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DIRS retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_insert"
+      "lbl" : "DIRS_YR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000910",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002288",
       "meta" : {
+        "definition" : {
+          "val" : "Ngaro retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs.",
+          "xrefs" : [ "PMID:24086727" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Ngaro YR retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ngaro retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RYN retrotransposon",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "orphan"
+      "lbl" : "Ngaro_YR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000912",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002285",
       "meta" : {
         "definition" : {
-          "val" : "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).",
-          "xrefs" : [ "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are 'CACTA/G…C/TAGTG'.",
+          "xrefs" : [ "PMID:26709091" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "asx turn",
+          "val" : "En transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DTC transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "dSpm transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CACTC transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CACTA TIR transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Spm transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CACTA transposon element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CMC-EnSpm transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "EnSpm transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "En-Spm transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00203"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "asx_turn"
+      "lbl" : "CACTA_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000911",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002286",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. YR retrotransposons have inverted terminal repeats (ITRs).",
+          "xrefs" : [ "PMID:24086727" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "predicted by ab initio computation",
+          "val" : "YR retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "tyrosine kinase retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "predicted_by_ab_initio_computation"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#aa3",
-      "type" : "PROPERTY",
-      "lbl" : "amino acid 3 letter code"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#aa1",
-      "type" : "PROPERTY",
-      "lbl" : "amino acid 1 letter code"
+      "lbl" : "YR_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000907",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002283",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature that has been predicted using sequence similarity techniques.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements favour insertion adjacent to TTAA.",
+          "xrefs" : [ "PMID:17984973" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "supported by sequence similarity",
+          "val" : "DTB transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "PiggyBac transposable element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "piggyBac TIR transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "supported_by_sequence_similarity"
+      "lbl" : "piggyBac_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000906",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002284",
       "meta" : {
         "definition" : {
-          "val" : "Attribute to describe a feature that is independently known - not predicted.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly 'TAA' or 'TTA'. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are 'GGG/CCC…GGC/GCC' or 'GA/GGCA…TGCC/TC'.",
+          "xrefs" : [ "PMID:26709091" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "independently known",
+          "val" : "PIF transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Harbinger transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Tourist transposon element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "PIF Harbinger TIR transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DTH transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "independently_known"
+      "lbl" : "PIF_Harbinger_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000909",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002281",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD).",
+          "xrefs" : [ "PMID:17984973" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "supported by EST or cDNA",
+          "val" : "Merlin TIR transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DTE transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Merlin transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "supported_by_EST_or_cDNA"
+      "lbl" : "Merlin_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000908",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002282",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature that has been predicted using sequence similarity of a known domain.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination.",
+          "xrefs" : [ "PMID:17984973" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "supported by domain match",
+          "val" : "DTR transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Transib TIR transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "transib transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "supported_by_domain_match"
+      "lbl" : "Transib_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000903",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002280",
       "meta" : {
+        "definition" : {
+          "val" : "Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent, either sharing only terminal G…C nucleotides, or with the G…C nucleotides absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification.",
+          "xrefs" : [ "PMID:17984973" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "endogenous retroviral sequence",
+          "val" : "Mutator transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "MULE",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mu transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "MLE transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "MuDR",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DTM transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mutator TIR transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "endogenous_retroviral_sequence"
+      "lbl" : "Mutator_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000902",
+      "id" : "http://purl.obolibrary.org/obo/so#evidence_for_feature",
       "meta" : {
         "definition" : {
-          "val" : "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "B is evidence_for_feature A, if an instance of B supports the existence of A.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Transgene"
-        } ],
+        "comments" : [ "This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "transgene"
+      "type" : "PROPERTY",
+      "lbl" : "evidence_for_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000905",
+      "id" : "http://purl.obolibrary.org/obo/so#derives_from",
       "meta" : {
-        "definition" : {
-          "val" : "An attribute describing the status of a feature, based on the available evidence.",
-          "xrefs" : [ "SO:ke" ]
-        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is the hypernym of attributes and should not be annotated to."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "status"
+      "type" : "PROPERTY",
+      "lbl" : "derives_from"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000904",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000099",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe the sequence of a feature, where the DNA is rearranged.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene from proviral sequence.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rearranged at DNA level",
+          "val" : "proviral gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -19195,106 +23192,200 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rearranged_at_DNA_level"
+      "lbl" : "proviral_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000901",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002278",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp.",
+          "xrefs" : [ "PMID:17984973", "PMID:8556864" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unequally crossed over",
+          "val" : "Stowaway",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TcMar-Stowaway transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Tc1 transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mariner",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DTT transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Tc1 Mariner TIR transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unequally_crossed_over"
+      "lbl" : "Tc1_Mariner_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000900",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000098",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene from plasmid sequence.",
+          "xrefs" : [ "SO:xp" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "plasmid gene",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "processed"
+      "lbl" : "plasmid_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#disconnected_from",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002279",
       "meta" : {
         "definition" : {
-          "val" : "X is disconnected_from Y iff it is not the case that X overlaps Y.",
-          "xrefs" : [ "PMID:20226267" ]
+          "val" : "The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb.",
+          "xrefs" : [ "PMID:11454746" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Ac transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "hAT transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ds transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "hAT-Ac transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "hAT TIR transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ac/Ds transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DTA transposon",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T01:42:10Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2020-06-25T14:00:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "disconnected_from"
+      "type" : "CLASS",
+      "lbl" : "hAT_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000939",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002276",
       "meta" : {
+        "definition" : {
+          "val" : "Short interspersed elements that originated from 5S rRNAs.",
+          "xrefs" : [ "PMID:21673742" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vertebrate immune system gene recombination signal feature",
+          "val" : "5S SINE element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5S SINE retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RSS retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immune_system_gene_recombination_signal_feature"
+      "lbl" : "5S_SINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000936",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002277",
       "meta" : {
+        "definition" : {
+          "val" : "Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules.",
+          "xrefs" : [ "PMID:22011512" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vertebrate immunoglobulin T cell receptor rearranged segment",
+          "val" : "DYC transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Crypton transposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Crypton YR transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment"
+      "lbl" : "Crypton_YR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000935",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000095",
       "meta" : {
         "definition" : {
-          "val" : "A CDS that is edited.",
+          "val" : "A plastid gene from leucoplast sequence.",
           "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "edited CDS",
+          "val" : "leucoplast gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -19303,79 +23394,142 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edited_CDS"
+      "lbl" : "leucoplast_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000938",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002274",
       "meta" : {
+        "definition" : {
+          "val" : "Short interspersed elements that originated from tRNAs.",
+          "xrefs" : [ "PMID:21673742" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vertebrate immunoglobulin T cell receptor rearranged gene cluster",
+          "val" : "tRNA SINE element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RST retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "tRNA SINE retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster"
+      "lbl" : "tRNA_SINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000937",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000094",
       "meta" : {
+        "definition" : {
+          "val" : "A gene from cyanelle sequence.",
+          "xrefs" : [ "SO:xp" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "cyanelle gene",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immune_system_feature"
+      "lbl" : "cyanelle_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000932",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002275",
       "meta" : {
+        "definition" : {
+          "val" : "Short interspersed elements that originated from 7SL RNAs.",
+          "xrefs" : [ "PMID:21673742" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pre-edited mRNA",
+          "val" : "7SL SINE element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RSL retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "7SL SINE retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pre_edited_mRNA"
+      "lbl" : "7SL_SINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000931",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002272",
       "meta" : {
         "definition" : {
-          "val" : "A region of a guide_RNA that base-pairs to a target mRNA.",
-          "xrefs" : [ "SO:jk" ]
+          "val" : "Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs.",
+          "xrefs" : [ "PMID:31709017" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "anchor region",
+          "val" : "L1 LINE retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "L1 element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "LINE-1 element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "LINE 1 element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "anchor_region"
+      "lbl" : "L1_LINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000934",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000097",
       "meta" : {
         "definition" : {
-          "val" : "A miRNA target site is a binding site where the molecule is a micro RNA.",
-          "xrefs" : [ "FB:cds" ]
+          "val" : "A gene from nucleomorph sequence.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miRNA target site",
+          "val" : "nucleomorph gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -19384,54 +23538,73 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miRNA_target_site"
+      "lbl" : "nucleomorph_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000933",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000096",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature between stages of processing.",
+          "val" : "A gene from proplastid sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "proplastid gene",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intermediate"
+      "lbl" : "proplastid_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000930",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002273",
       "meta" : {
         "definition" : {
-          "val" : "A region of guide RNA.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
+        "xrefs" : [ {
+          "val" : "https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/long-interspersed-nuclear-element"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "guide RNA region",
+          "val" : "I LINE retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "LINE I element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RII retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "guide_RNA_region"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#AAMOD",
-      "type" : "PROPERTY",
-      "lbl" : "amino acid modification"
+      "lbl" : "I_LINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000929",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000091",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA that is edited.",
+          "val" : "A gene from apicoplast sequence.",
           "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "edited mRNA",
+          "val" : "apicoplast gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -19440,643 +23613,828 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edited_mRNA"
+      "lbl" : "apicoplast_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000928",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002270",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a AA dinucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain.",
+          "xrefs" : [ "PMID:9729877" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert AA",
+          "val" : "RIT retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RTE LINE retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RTE retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_AA"
+      "lbl" : "RTE_LINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000925",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000090",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a GU dinucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene from plastid sequence.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert GU",
+          "val" : "plastid gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_GU"
+      "lbl" : "plastid_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000924",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002271",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a GC dinucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT).",
+          "xrefs" : [ "PMID:31709017" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert GC",
+          "val" : "Jockey LINE retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "LINE Jockey element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RIJ retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_GC"
+      "lbl" : "Jockey_LINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000927",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000093",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a AU dinucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene from chromoplast_sequence.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert AU",
+          "val" : "chromoplast gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_AU"
+      "lbl" : "chromoplast_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000926",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000092",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a CU dinucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene from chloroplast sequence.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert CU",
+          "val" : "chloroplast gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ct gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_CU"
+      "lbl" : "ct_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000921",
+      "id" : "http://purl.obolibrary.org/obo/so#dbvar",
+      "lbl" : "DBVAR"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002269",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a dinucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes.",
+          "xrefs" : [ "PMID:21734471" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert dinucleotide",
+          "val" : "RIR retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "R2 LINE retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "R2 retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_dinucleotide"
+      "lbl" : "R2_LINE_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000920",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002298",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a cytidine.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An operon whose transcription is coordinated on a single transcription unit.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
         },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert C",
+          "val" : "simple operon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_C"
+      "lbl" : "simple_operon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000923",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002299",
       "meta" : {
         "definition" : {
-          "val" : "An edit to insert a G.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An operon whose transcription is coordinated on several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
         },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insert G",
+          "val" : "complex operon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insert_G"
+      "lbl" : "complex_operon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000922",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002296",
       "meta" : {
         "definition" : {
-          "val" : "An edit to substitute an U for a C.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter. ",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
         },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "substitute C to U",
+          "val" : "transcription factor regulatory site phrase",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "transcription factor regulatory site module",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TFRS phrase",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TFRS module",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "substitute_C_to_U"
+      "lbl" : "TFRS_module"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002297",
       "meta" : {
         "definition" : {
-          "val" : "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).",
-          "xrefs" : [ "PMID:20226267" ]
+          "val" : "The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
         },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "TFRS collection",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "transcription factor regulatory site collection",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "david"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: region is consecutive_sequence of base."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T02:19:48Z"
+          "val" : "2020-08-05T11:49:30Z"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "is_consecutive_sequence_of"
+      "type" : "CLASS",
+      "lbl" : "TFRS_collection"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000016",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002294",
       "meta" : {
         "definition" : {
-          "val" : "A transition of a guanine to an adenine.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Mitochondrial displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "Added as per request by Terence Murphy (INSDC) for GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/D_loop"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "G to A transition",
+          "val" : "Mitochondrial D loop",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mitochondrial displacement loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-07-08T11:49:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "G_to_A_transition"
+      "lbl" : "mitochondrial_D_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000015",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002295",
       "meta" : {
         "definition" : {
-          "val" : "A transition of an adenine to a guanine.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A TF_binding_site that is involved in regulation of expression.",
+          "xrefs" : [ "Bacterial_regulation_working_group:CMA", "PMID:32665585" ]
         },
+        "comments" : [ "Added as per Mejia-Almonte et.al PMID:32665585" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "A to G transition",
+          "val" : "transcription factor regulatory site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TFRS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-08-05T11:49:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "A_to_G_transition"
+      "lbl" : "transcription_factor_regulatory_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000014",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002292",
       "meta" : {
         "definition" : {
-          "val" : "A substitution of a purine, A or G, for another purine.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail.",
+          "xrefs" : [ "PMID:29086764", "PMID:29182528", "PMID:29576969" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "purine transition",
+          "val" : "circular mRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "coding circRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-07-01T11:49:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "purine_transition"
+      "lbl" : "circular_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000013",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002293",
       "meta" : {
+        "definition" : {
+          "val" : "The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis.",
+          "xrefs" : [ "PMID: 19407924", "PMID:10968878" ]
+        },
+        "comments" : [ "Added as per GitHub Issue Request #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417) from INSDC" ],
+        "xrefs" : [ {
+          "val" : "https://en.wikipedia.org/wiki/MtDNA_control_region"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T to C transition",
+          "val" : "Mitochondrial noncoding region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "MtDNA control region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mitochondrial DNA control region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mitochondrial NCR",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "MtDNA_control_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mitochondrial A+T region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-07-01T16:40:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "T_to_C_transition"
+      "lbl" : "mitochondrial_control_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000019",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002290",
       "meta" : {
         "definition" : {
-          "val" : "A transversion from cytidine to adenine.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease.",
+          "xrefs" : [ "PMID:23914310" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #488 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/488)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "C to A transversion",
+          "val" : "Penelope retrotransposon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RPP retrotransposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-06-25T14:00:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "C_to_A_transversion"
+      "lbl" : "Penelope_retrotransposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000018",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002291",
       "meta" : {
         "definition" : {
-          "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non-coding RNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail.",
+          "xrefs" : [ "PMID:29086764", "PMID:29182528", "PMID:29230098", "PMID:29576969", "PMID:29626935" ]
         },
+        "comments" : [ "Added as per GitHub Issue Request #490 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/490) and GitHub Issue Request #391 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/391)" ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "circRNA",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "pyrimidine to purine transversion",
+          "val" : "circular ncRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "noncoding circRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "david"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2020-07-01T11:49:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pyrimidine_to_purine_transversion"
+      "lbl" : "circular_ncRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000017",
+      "id" : "http://purl.obolibrary.org/obo/so#has_part",
       "meta" : {
         "definition" : {
-          "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "Inverse of part_of.",
+          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Transversion"
-        } ],
+        "comments" : [ "Example: operon has_part gene." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "transversion"
+      "type" : "PROPERTY",
+      "lbl" : "has_part"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000837",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000092",
       "meta" : {
         "definition" : {
-          "val" : "A region of UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing complex change of translational product",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "UTR region",
+          "val" : "sequence variant causing complex change of translational product",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001539"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "UTR_region"
+      "lbl" : "sequence_variant_causing_complex_change_of_translational_product"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000836",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000091",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_1000088"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000090",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_1000088"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000096",
       "meta" : {
         "definition" : {
-          "val" : "A region of an mRNA.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing amino acid insertion",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "mRNA region",
+          "val" : "sequence variant causing amino acid insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root."
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001605"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_region"
+      "lbl" : "sequence_variant_causing_amino_acid_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000839",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000095",
       "meta" : {
-        "definition" : {
-          "val" : "Biological sequence region that can be assigned to a specific subsequence of a polypeptide.",
-          "xrefs" : [ "SO:GAR", "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "region or site annotation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "site",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "positional polypeptide feature",
+          "val" : "mutation causing nonconservative amino acid substitution",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "region",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "positional",
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing nonconservative amino acid substitution",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00124"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00331"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added to allow the polypeptide regions to have is_a paths back to the root."
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001607"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_region"
+      "lbl" : "sequence_variant_causing_nonconservative_amino_acid_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000838",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000094",
       "meta" : {
-        "definition" : {
-          "val" : "A region of an rRNA primary transcript.",
-          "xrefs" : [ "SO:ke" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing conservative amino acid substitution",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA primary transcript region",
+          "val" : "sequence variant causing conservative amino acid substitution",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001607"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "To allow transcribed_spacer_region to have a path to the root."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_primary_transcript_region"
+      "lbl" : "sequence_variant_causing_conservative_amino_acid_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000833",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000093",
       "meta" : {
         "definition" : {
-          "val" : "A region of a transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The replacement of a single amino acid by another.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript region",
+          "val" : "sequence variant causing amino acid substitution",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing amino acid substitution",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root."
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001606"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "transcript_region"
+      "lbl" : "sequence_variant_causing_amino_acid_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000832",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000099",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence which is part of a promoter.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing polypeptide elongation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing polypeptide elongation",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is a manufactured term to allow the parts of promoter to have an is_a path back to the root."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001609"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "promoter_region"
+      "lbl" : "sequence_variant_causing_polypeptide_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000835",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000098",
       "meta" : {
         "definition" : {
-          "val" : "A part of a primary transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062).",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "primary transcript region",
+          "val" : "sequence variant causing polypeptide truncation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing polypeptide truncation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root."
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001587"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "primary_transcript_region"
+      "lbl" : "sequence_variant_causing_polypeptide_truncation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000834",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000097",
       "meta" : {
         "definition" : {
-          "val" : "A region of a mature transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing amino acid deletion",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "mature transcript region",
+          "val" : "sequence variant causing amino acid deletion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root."
-        } ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001825"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "mature_transcript_region"
+      "lbl" : "sequence_variant_causing_amino_acid_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000023",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000918",
       "meta" : {
         "definition" : {
-          "val" : "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.",
+          "val" : "An edit to delete a uridine.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "purine to pyrimidine transversion",
+          "val" : "delete U",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "purine_to_pyrimidine_transversion"
+      "lbl" : "delete_U"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000022",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000917",
       "meta" : {
         "definition" : {
-          "val" : "A transversion from T to G.",
+          "val" : "An edit to insert a U.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T to G transversion",
+          "val" : "insert U",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "T_to_G_transversion"
+      "lbl" : "insert_U"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000831",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000919",
       "meta" : {
         "definition" : {
-          "val" : "A region of a gene.",
+          "val" : "An edit to substitute an I for an A.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene member region",
+          "val" : "substitute A to I",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A manufactured term used to allow the parts of a gene to have an is_a path to the root."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "gene_member_region"
+      "lbl" : "substitute_A_to_I"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000021",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000914",
       "meta" : {
         "definition" : {
-          "val" : "A transversion from T to A.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A clone insert made from genomic DNA.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T to A transversion",
+          "val" : "cloned genomic insert",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20085,13 +24443,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "T_to_A_transversion"
+      "lbl" : "cloned_genomic_insert"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000020",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000913",
       "meta" : {
+        "definition" : {
+          "val" : "A clone insert made from cDNA.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "C to G transversion",
+          "val" : "cloned cDNA insert",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20100,41 +24462,33 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "C_to_G_transversion"
+      "lbl" : "cloned_cDNA_insert"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000830",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000916",
       "meta" : {
-        "definition" : {
-          "val" : "A region of a chromosome.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromosome part",
+          "val" : "edit operation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "chromosome_part"
+      "lbl" : "edit_operation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000005",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000915",
       "meta" : {
         "definition" : {
-          "val" : "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A clone insert that is engineered.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "complex substitution",
+          "val" : "engineered insert",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20143,53 +24497,54 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "complex_substitution"
+      "lbl" : "engineered_insert"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000002",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000910",
       "meta" : {
         "definition" : {
-          "val" : "A sequence alteration where the length of the change in the variant is the same as that of the reference.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "loinc:LA6690-7"
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "substitution"
+      "lbl" : "orphan"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000009",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000912",
       "meta" : {
         "definition" : {
-          "val" : "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).",
+          "xrefs" : [ "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "asx turn",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00203"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transition"
+      "lbl" : "asx_turn"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000008",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000911",
       "meta" : {
         "definition" : {
-          "val" : "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.",
-          "xrefs" : [ "SO:immuno_workshop" ]
+          "val" : "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Point_mutation"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "point mutation",
+          "val" : "predicted by ab initio computation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20198,17 +24553,23 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "point_mutation"
+      "lbl" : "predicted_by_ab_initio_computation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000829",
+      "id" : "http://purl.obolibrary.org/obo/so#aa3",
+      "lbl" : "amino acid 3 letter code"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#aa1",
+      "lbl" : "amino acid 1 letter code"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000907",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a nucleomorph.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute to describe a feature that has been predicted using sequence similarity techniques.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nucleomorphic chromosome",
+          "val" : "supported by sequence similarity",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20217,17 +24578,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nucleomorphic_chromosome"
+      "lbl" : "supported_by_sequence_similarity"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000825",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000906",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a micronucleus.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "Attribute to describe a feature that is independently known - not predicted.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "micronuclear chromosome",
+          "val" : "independently known",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20236,17 +24597,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "micronuclear_chromosome"
+      "lbl" : "independently_known"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000828",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000909",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a nucleus.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nuclear chromosome",
+          "val" : "supported by EST or cDNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20255,17 +24616,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclear_chromosome"
+      "lbl" : "supported_by_EST_or_cDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000822",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000908",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a cyanelle.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute to describe a feature that has been predicted using sequence similarity of a known domain.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cyanelle chromosome",
+          "val" : "supported by domain match",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20274,17 +24635,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cyanelle_chromosome"
+      "lbl" : "supported_by_domain_match"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000821",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000903",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a chromoplast.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "Endogenous DNA sequence that are likely to have arisen from retroviruses.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromoplast chromosome",
+          "val" : "endogenous retroviral sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20293,22 +24654,16 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromoplast_chromosome"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym",
-      "type" : "PROPERTY",
-      "lbl" : "has_related_synonym"
+      "lbl" : "endogenous_retroviral_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000824",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000902",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a macronucleus.",
+          "val" : "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another.",
           "xrefs" : [ "SO:xp" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "macronuclear chromosome",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Transgene"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -20316,36 +24671,32 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "macronuclear_chromosome"
+      "lbl" : "transgene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000823",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000905",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome with origin in a leucoplast.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute describing the status of a feature, based on the available evidence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "leucoplast chromosome",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This term is the hypernym of attributes and should not be annotated to." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "leucoplast_chromosome"
+      "lbl" : "status"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000012",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000904",
       "meta" : {
         "definition" : {
-          "val" : "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An attribute to describe the sequence of a feature, where the DNA is rearranged.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "C to T transition at pCpG site",
+          "val" : "rearranged at DNA level",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20354,74 +24705,124 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "C_to_T_transition_at_pCpG_site"
+      "lbl" : "rearranged_at_DNA_level"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000011",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000901",
       "meta" : {
         "definition" : {
-          "val" : "A transition of a cytidine to a thymine.",
+          "val" : "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "C to T transition",
+          "val" : "unequally crossed over",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "C_to_T_transition"
+      "lbl" : "unequally_crossed_over"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000820",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000900",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a chloroplast.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "chloroplast chromosome",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "chloroplast_chromosome"
+      "lbl" : "processed"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000010",
+      "id" : "http://purl.obolibrary.org/obo/so#disconnected_from",
       "meta" : {
         "definition" : {
-          "val" : "A substitution of a pyrimidine, C or T, for another pyrimidine.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "X is disconnected_from Y iff it is not the case that X overlaps Y.",
+          "xrefs" : [ "PMID:20226267" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "pyrimidine transition",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T01:42:10Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "pyrimidine_transition"
+      "type" : "PROPERTY",
+      "lbl" : "disconnected_from"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000038",
+      "id" : "http://purl.obolibrary.org/obo/BS_00070",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001068"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00073",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001149"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00072",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001084"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00071",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001147"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000939",
       "meta" : {
         "definition" : {
-          "val" : "A duplication that occurred within a chromosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Feature used for the recombination of genomic material for the purpose of generating diversity of the immune system.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "intrachromosomal duplication",
+          "val" : "vertebrate immune system gene recombination signal feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20430,28 +24831,43 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intrachromosomal_duplication"
+      "lbl" : "vertebrate_immune_system_gene_recombination_signal_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000037",
+      "id" : "http://purl.obolibrary.org/obo/BS_00077",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001062"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00076",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001064"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000936",
       "meta" : {
         "definition" : {
-          "val" : "An extra chromosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Chromosomal_duplication"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(fungi)Dp",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "chromosomal duplication",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)Dp",
+          "val" : "vertebrate immunoglobulin T cell receptor rearranged segment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20460,22 +24876,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_duplication"
+      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000036",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000935",
       "meta" : {
         "definition" : {
-          "val" : "A continuous nucleotide sequence is inverted in the same position.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A CDS that is edited.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR", "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "loinc:LA6689-9"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inversion",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
+          "val" : "edited CDS",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -20483,16 +24895,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inversion"
+      "lbl" : "edited_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000860",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000938",
       "meta" : {
         "definition" : {
-          "val" : "Attribute describing sequence regions occurring in same order on chromosome of different species.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Syntenic"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "vertebrate immunoglobulin T cell receptor rearranged gene cluster",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -20500,43 +24914,28 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "syntenic"
+      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000035",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000937",
       "meta" : {
-        "definition" : {
-          "val" : "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html", "NCBI:th" ]
-        },
-        "xrefs" : [ {
-          "val" : "loinc:LA6686-5"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "nucleotide duplication",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "nucleotide_duplication",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "duplication"
+      "lbl" : "vertebrate_immune_system_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000039",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000932",
       "meta" : {
         "definition" : {
-          "val" : "A tandem duplication where the individual regions are in the same orientation.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A primary transcript that, at least in part, encodes one or more proteins that has not been edited.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "direct tandem duplication",
+          "val" : "pre-edited mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -20545,64 +24944,50 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "direct_tandem_duplication"
+      "lbl" : "pre_edited_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001709",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000931",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "A region of a guide_RNA that base-pairs to a target mRNA.",
+          "xrefs" : [ "SO:jk" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K27Me3",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K27 tri-methylation site",
+          "val" : "anchor region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:32:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K27_trimethylation_site"
+      "lbl" : "anchor_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#overlaps",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000934",
       "meta" : {
         "definition" : {
-          "val" : "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.",
-          "xrefs" : [ "PMID:20226267" ]
+          "val" : "A miRNA target site is a binding site where the molecule is a micro RNA.",
+          "xrefs" : [ "FB:cds" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "miRNA target site",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: coding_exon overlaps CDS."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T01:33:15Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "overlaps"
+      "type" : "CLASS",
+      "lbl" : "miRNA_target_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000859",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000933",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a kind of homology where divergence occurred after a duplication event.",
+          "val" : "An attribute to describe a feature between stages of processing.",
           "xrefs" : [ "SO:ke" ]
         },
         "basicPropertyValues" : [ {
@@ -20611,410 +24996,321 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "paralogous"
+      "lbl" : "intermediate"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001706",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000930",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "A region of guide RNA.",
+          "xrefs" : [ "SO:ma" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K4 tri-methylation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K4me3",
+          "val" : "guide RNA region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:29:12Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K4_trimethylation"
+      "lbl" : "guide_RNA_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001705",
+      "id" : "http://purl.obolibrary.org/obo/so#AAMOD",
+      "lbl" : "amino acid modification"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000929",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "An mRNA that is edited.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K4 mono-methylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K4me1",
+          "val" : "edited mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:28:14Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K4_monomethylation_site"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#has_origin",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "has_origin"
+      "lbl" : "edited_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000858",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000928",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a kind of homology where divergence occurred after a speciation event.",
+          "val" : "An edit to insert a AA dinucleotide.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "insert AA",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "orthologous"
+      "lbl" : "insert_AA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001708",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000925",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "An edit to insert a GU dinucleotide.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H2K27Me1",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2K27 mono-methylation site",
+          "val" : "insert GU",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:31:54Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "H3K27_monomethylation_site"
+      "lbl" : "insert_GU"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001707",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000924",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "An edit to insert a GC dinucleotide.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K9Me3",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K9 tri-methylation site",
+          "val" : "insert GC",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:30:34Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "H3K9_trimethylation_site"
+      "lbl" : "insert_GC"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001702",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000927",
       "meta" : {
         "definition" : {
-          "val" : "A histone modification where the modification is the acylation of the residue.",
+          "val" : "An edit to insert a AU dinucleotide.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histone acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "histone acetylation",
+          "val" : "insert AU",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:23:27Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "histone_acetylation_site"
+      "lbl" : "insert_AU"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000041",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000926",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome structure variation whereby a transposition occurred within a chromosome.",
+          "val" : "An edit to insert a CU dinucleotide.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "intrachromosomal transposition",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)Tp",
+          "val" : "insert CU",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "intrachromosomal_transposition"
+      "lbl" : "insert_CU"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000855",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000921",
       "meta" : {
         "definition" : {
-          "val" : "A homologous_region that is orthologous to another region.",
+          "val" : "An edit to insert a dinucleotide.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Ortholog#Orthology"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "orthologous region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "orthologue",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ortholog",
+          "val" : "insert dinucleotide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term should be used in conjunction with the similarity relationships defined in SO."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "orthologous_region"
+      "lbl" : "insert_dinucleotide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000040",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000920",
       "meta" : {
         "definition" : {
-          "val" : "A tandem duplication where the individual regions are not in the same orientation.",
+          "val" : "An edit to insert a cytidine.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mirror duplication",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "inverted tandem duplication",
+          "val" : "insert C",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "inverted_tandem_duplication"
+      "lbl" : "insert_C"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000854",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000923",
       "meta" : {
         "definition" : {
-          "val" : "A homologous_region that is paralogous to another region.",
+          "val" : "An edit to insert a G.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Paralog#Paralogy"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "paralogous region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "paralogue",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "paralog",
+          "val" : "insert G",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A term to be used in conjunction with the paralogous_to relationship."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "paralogous_region"
+      "lbl" : "insert_G"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001701",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000922",
       "meta" : {
         "definition" : {
-          "val" : "A histone modification site where the modification is the methylation of the residue.",
+          "val" : "An edit to substitute an U for a C.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histone methylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "histone methylation",
+          "val" : "substitute C to U",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:23:02Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "histone_methylation_site"
+      "lbl" : "substitute_C_to_U"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001704",
+      "id" : "http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical).",
+          "xrefs" : [ "PMID:20226267" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K14ac",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K14 acetylation site",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Example: region is consecutive_sequence of base." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:25:53Z"
+          "val" : "2010-10-14T02:19:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "H3K14_acetylation_site"
+      "type" : "PROPERTY",
+      "lbl" : "is_consecutive_sequence_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000857",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000016",
       "meta" : {
         "definition" : {
-          "val" : "Similarity due to common ancestry.",
+          "val" : "A transition of a guanine to an adenine.",
           "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "G to A transition",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "homologous"
+      "lbl" : "G_to_A_transition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001703",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000015",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "A transition of an adenine to a guanine.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K9 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K9ac",
+          "val" : "A to G transition",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:25:05Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K9_acetylation_site"
+      "lbl" : "A_to_G_transition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000856",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000014",
       "meta" : {
+        "definition" : {
+          "val" : "A substitution of a purine, A or G, for another purine.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "purine transition",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conserved"
+      "lbl" : "purine_transition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000851",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000013",
       "meta" : {
         "definition" : {
-          "val" : "A region of a CDS.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A transition of a thymine to a cytidine.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CDS region",
+          "val" : "T to C transition",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21023,28 +25319,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CDS_region"
+      "lbl" : "T_to_C_transition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000045",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000019",
       "meta" : {
         "definition" : {
-          "val" : "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Ring_chromosome" ]
+          "val" : "A transversion from cytidine to adenine.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Ring_chromosome"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(fungi)C",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)R",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "ring chromosome",
+          "val" : "C to A transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21053,28 +25338,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ring_chromosome"
+      "lbl" : "C_to_A_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000044",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000018",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Chromosomal_translocation"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)T",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(fungi)T",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "chromosomal translocation",
+          "val" : "pyrimidine to purine transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21083,18 +25357,16 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_translocation"
+      "lbl" : "pyrimidine_to_purine_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000850",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000017",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "five prime LTR component",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5' long term repeat component",
-          "xrefs" : [ ]
+        "definition" : {
+          "val" : "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Transversion"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -21102,28 +25374,45 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_LTR_component"
+      "lbl" : "transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000853",
+      "id" : "http://purl.obolibrary.org/obo/BS_00052",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001089"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00055",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000725"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000837",
       "meta" : {
         "definition" : {
-          "val" : "A region that is homologous to another region.",
+          "val" : "A region of UTR.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Homology_(biology)"
-        } ],
+        "comments" : [ "A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "homolog",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "homologue",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "homologous region",
+          "val" : "UTR region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21132,28 +25421,19 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "homologous_region"
+      "lbl" : "UTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000043",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000836",
       "meta" : {
         "definition" : {
-          "val" : "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Robertsonian_translocation" ]
+          "val" : "A region of an mRNA.",
+          "xrefs" : [ "SO:cb" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Robertsonian_fusion"
-        } ],
+        "comments" : [ "This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "whole-arm translocations",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "centric-fusion translocations",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Robertsonian fusion",
+          "val" : "mRNA region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21162,70 +25442,61 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Robertsonian_fusion"
+      "lbl" : "mRNA_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#finished_by",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000839",
       "meta" : {
         "definition" : {
-          "val" : "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.",
-          "xrefs" : [ "PMID:20226267" ]
+          "val" : "Biological sequence region that can be assigned to a specific subsequence of a polypeptide.",
+          "xrefs" : [ "SO:GAR", "SO:ke" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+        "comments" : [ "Added to allow the polypeptide regions to have is_a paths back to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasNarrowSynonym",
+          "val" : "site",
+          "xrefs" : [ "uniprot:feature_type" ]
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example CDS finished_by stop_codon."
+          "pred" : "hasRelatedSynonym",
+          "val" : "positional",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T01:45:45Z"
+          "pred" : "hasNarrowSynonym",
+          "val" : "region",
+          "xrefs" : [ "uniprot:feature_type" ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "finished_by"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001700",
-      "meta" : {
-        "definition" : {
-          "val" : "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.",
-          "xrefs" : [ "http:en.wikipedia.org/wiki/Histone" ]
-        },
-        "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "histone modification site",
+          "val" : "region or site annotation",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "histone modification",
+          "pred" : "hasRelatedSynonym",
+          "val" : "positional polypeptide feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:22:08Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00331"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00124"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histone_modification"
+      "lbl" : "polypeptide_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000852",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000838",
       "meta" : {
         "definition" : {
-          "val" : "A region of an exon.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A region of an rRNA primary transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "To allow transcribed_spacer_region to have a path to the root." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "exon region",
+          "val" : "rRNA primary transcript region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21234,17 +25505,19 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exon_region"
+      "lbl" : "rRNA_primary_transcript_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000042",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000833",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms.",
+          "val" : "A region of a transcript.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "compound chromosome",
+          "val" : "transcript region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21253,36 +25526,35 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "compound_chromosome"
+      "lbl" : "transcript_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000027",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000832",
       "meta" : {
         "definition" : {
-          "val" : "A transversion from guanine to thymine.",
+          "val" : "A region of sequence which is part of a promoter.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "G to T transversion",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This is a manufactured term to allow the parts of promoter to have an is_a path back to the root." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "G_to_T_transversion"
+      "lbl" : "promoter_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000026",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000835",
       "meta" : {
         "definition" : {
-          "val" : "A transversion from guanine to cytidine.",
+          "val" : "A part of a primary transcript.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "G to C transversion",
+          "val" : "primary transcript region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21291,17 +25563,19 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "G_to_C_transversion"
+      "lbl" : "primary_transcript_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000025",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000834",
       "meta" : {
         "definition" : {
-          "val" : "A transversion from adenine to thymine.",
+          "val" : "A region of a mature transcript.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "A to T transversion",
+          "val" : "mature transcript region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21310,17 +25584,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "A_to_T_transversion"
+      "lbl" : "mature_transcript_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000024",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000023",
       "meta" : {
         "definition" : {
-          "val" : "A transversion from adenine to cytidine.",
+          "val" : "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "A to C transversion",
+          "val" : "purine to pyrimidine transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21329,36 +25603,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "A_to_C_transversion"
+      "lbl" : "purine_to_pyrimidine_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000029",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000022",
       "meta" : {
         "definition" : {
-          "val" : "An incomplete chromosome.",
+          "val" : "A transversion from T to G.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Chromosomal_deletion"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(bacteria)&ampDgr;",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(fungi)D",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)Df",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "chromosomal deletion",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "deficiency",
+          "val" : "T to G transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21367,17 +25622,19 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_deletion"
+      "lbl" : "T_to_G_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000028",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000831",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal structure variation within a single chromosome.",
+          "val" : "A region of a gene.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A manufactured term used to allow the parts of a gene to have an is_a path to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "intrachromosomal mutation",
+          "val" : "gene member region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21386,27 +25643,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intrachromosomal_mutation"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#sequence_of",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "sequence_of"
+      "lbl" : "gene_member_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000848",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000021",
       "meta" : {
+        "definition" : {
+          "val" : "A transversion from T to A.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "long term repeat component",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "LTR component",
+          "val" : "T to A transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21415,39 +25662,46 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "LTR_component"
+      "lbl" : "T_to_A_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000847",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000020",
       "meta" : {
         "definition" : {
-          "val" : "A region of a tmRNA.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A transversion of a cytidine to a guanine.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tmRNA region",
+          "val" : "C to G transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tmRNA_region"
+      "lbl" : "C_to_G_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000849",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000830",
       "meta" : {
+        "definition" : {
+          "val" : "A region of a chromosome.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime LTR component",
+          "val" : "chromosome part",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "3' long terminal repeat component",
+          "val" : "chromosomal_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "chromosomal region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21456,53 +25710,50 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_LTR_component"
+      "lbl" : "chromosome_part"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000844",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000005",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence which is a promoter for RNA polymerase II.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "complex substitution",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNApol_II_promoter_region"
+      "lbl" : "complex_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000030",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000004",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001059"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000002",
       "meta" : {
         "definition" : {
-          "val" : "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.",
+          "val" : "A sequence alteration where the length of the change in the variant is the same as that of the reference.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Chromosomal_inversion"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(bacteria)IN",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(fungi)In",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "chromosomal inversion",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)In",
-          "xrefs" : [ ]
+          "val" : "loinc:LA6690-7"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -21510,118 +25761,125 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_inversion"
+      "lbl" : "substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000843",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000009",
       "meta" : {
         "definition" : {
-          "val" : "A region which is part of a bacterial RNA polymerase promoter.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bacterial_RNApol_promoter_region"
+      "lbl" : "transition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000846",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000008",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence which is a promoter for RNA polymerase III type 2.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence.",
+          "xrefs" : [ "SO:immuno_workshop" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Point_mutation"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "point mutation",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNApol_III_promoter_type_2_region"
+      "lbl" : "point_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000845",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000007",
       "meta" : {
-        "definition" : {
-          "val" : "A region of sequence which is a promoter for RNA polymerase III type 1.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root."
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001059"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00063",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001061"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "RNApol_III_promoter_type_1_region"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000840",
+      "id" : "http://purl.obolibrary.org/obo/BS_00067",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000691"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000829",
       "meta" : {
         "definition" : {
-          "val" : "A region of a repeated sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosome originating in a nucleomorph.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "repeat component",
+          "val" : "nucleomorphic chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A manufactured to group the parts of repeats, to give them an is_a path back to the root."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "repeat_component"
+      "lbl" : "nucleomorphic_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000032",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000826",
       "meta" : {
-        "definition" : {
-          "val" : "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html", "http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel" ]
-        },
-        "xrefs" : [ {
-          "val" : "loinc:LA9659-9"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Indel"
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Indels can have a different number of bases than the corresponding reference sequence."
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000741"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "indel"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000842",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000825",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "definition" : {
+          "val" : "A chromosome originating in a micronucleus.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene component region",
+          "val" : "micronuclear chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21630,40 +25888,75 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_component_region"
+      "lbl" : "micronuclear_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000841",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000828",
       "meta" : {
         "definition" : {
-          "val" : "A region within an intron.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosome originating in a nucleus.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "spliceosomal intron region",
+          "val" : "nuclear chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A terms added to allow the parts of introns to have is_a paths to the root."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "spliceosomal_intron_region"
+      "lbl" : "nuclear_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000031",
+      "id" : "http://purl.obolibrary.org/obo/BS_00069",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001085"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00068",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001066"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000827",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000742"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000822",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal structure variation whereby more than one chromosome is involved.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosome originating in a cyanelle.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "interchromosomal mutation",
+          "val" : "cyanelle chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21672,99 +25965,78 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "interchromosomal_mutation"
+      "lbl" : "cyanelle_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000880",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000821",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence that contains the code for more than one gene product.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosome originating in a chromoplast.",
+          "xrefs" : [ "SO:xp" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "chromoplast chromosome",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polycistronic"
+      "lbl" : "chromoplast_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000059",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym",
+      "type" : "PROPERTY",
+      "lbl" : "has_related_synonym"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000824",
       "meta" : {
         "definition" : {
-          "val" : "The nucleotide change in the codon leads to a new codon coding for a new amino acid.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A chromosome originating in a macronucleus.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing missense codon change in transcript",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing missense codon change in transcript",
+          "val" : "macronuclear chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001583"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_missense_codon_change_in_transcript"
+      "lbl" : "macronuclear_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000058",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000823",
       "meta" : {
         "definition" : {
-          "val" : "A DNA point mutation that causes a substitution of an amino acid by an other.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A chromosome with origin in a leucoplast.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing non synonymous codon change in transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non-synonymous codon change in transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing non synonymous codon change in transcript",
+          "val" : "leucoplast chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001583"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_non_synonymous_codon_change_in_transcript"
+      "lbl" : "leucoplast_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000882",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000012",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing the alteration of codon meaning.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "codon redefined",
+          "val" : "C to T transition at pCpG site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -21773,151 +26045,129 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "codon_redefined"
+      "lbl" : "C_to_T_transition_at_pCpG_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000057",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000011",
       "meta" : {
         "definition" : {
-          "val" : "The changed codon has the same translation product as the original codon.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A transition of a cytidine to a thymine.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing synonymous codon change in transcript",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing synonymous codon change in transcript",
+          "val" : "C to T transition",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001819"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_synonymous_codon_change_in_transcript"
+      "lbl" : "C_to_T_transition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000881",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000010",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.",
+          "val" : "A substitution of a pyrimidine, C or T, for another pyrimidine.",
           "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "pyrimidine transition",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recoded"
+      "lbl" : "pyrimidine_transition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001728",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000820",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosome originating in a chloroplast.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K9 di-methylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K9Me2",
+          "val" : "chloroplast chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:08:19Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K9_dimethylation_site"
+      "lbl" : "chloroplast_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001727",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000038",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.",
+          "val" : "A duplication that occurred within a chromosome.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K9 mono-methylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K9Me1",
+          "val" : "intrachromosomal duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:06:17Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K9_monomethylation_site"
+      "lbl" : "intrachromosomal_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001729",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000037",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated.",
+          "val" : "An extra chromosome.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Chromosomal_duplication"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H4K16 acetylation site",
+          "val" : "chromosomal duplication",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H4K16ac",
+          "pred" : "hasRelatedSynonym",
+          "val" : "(fungi)Dp",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)Dp",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:09:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4K16_acetylation_site"
+      "lbl" : "chromosomal_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000877",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000036",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a situation where a gene may encode for more than 1 transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A continuous nucleotide sequence is inverted in the same position.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR", "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "loinc:LA6689-9"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "alternatively spliced",
-          "xrefs" : [ ]
+          "val" : "inversion",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbvar"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -21925,78 +26175,60 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alternatively_spliced"
+      "lbl" : "inversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000063",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000860",
       "meta" : {
         "definition" : {
-          "val" : "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence.",
+          "val" : "Attribute describing sequence regions occurring in same order on chromosome of different species.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing terminator codon change in transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing terminator codon change in transcript",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Syntenic"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001590"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_terminator_codon_change_in_transcript"
+      "lbl" : "syntenic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001724",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000035",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html", "NCBI:th" ]
         },
+        "xrefs" : [ {
+          "val" : "loinc:LA6686-5"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K36 tri-methylation site",
+          "val" : "nucleotide duplication",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "H3K36Me3",
+          "val" : "nucleotide_duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:01:58Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K36_trimethylation_site"
+      "lbl" : "duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000876",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000039",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence that is bound by a nucleic acid.",
+          "val" : "A tandem duplication where the individual regions are in the same orientation.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bound by nucleic acid",
+          "val" : "direct tandem duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22005,134 +26237,160 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bound_by_nucleic_acid"
+      "lbl" : "direct_tandem_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001723",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001709",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "H3K36Me2",
+          "val" : "H3K27Me3",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K36 di-methylation site",
+          "val" : "H3K27 tri-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T10:59:35Z"
+          "val" : "2010-03-31T10:32:41Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "H3K27_trimethylation_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00033",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000409"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00032",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001067"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#overlaps",
+      "meta" : {
+        "definition" : {
+          "val" : "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y.",
+          "xrefs" : [ "PMID:20226267" ]
+        },
+        "comments" : [ "Example: coding_exon overlaps CDS." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T01:33:15Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "H3K36_dimethylation_site"
+      "type" : "PROPERTY",
+      "lbl" : "overlaps"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000062",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001706",
       "meta" : {
         "definition" : {
-          "val" : "The nucleotide change in the codon triplet creates a terminator codon.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing nonsense codon change in transcript",
+          "val" : "H3K4 tri-methylation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing nonsense codon change in transcript",
+          "val" : "H3K4me3",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001587"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:29:12Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_nonsense_codon_change_in_transcript"
+      "lbl" : "H3K4_trimethylation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000061",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000859",
       "meta" : {
         "definition" : {
-          "val" : "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An attribute describing a kind of homology where divergence occurred after a duplication event.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing nonconservative missense codon change in transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing nonconservative missense codon change in transcript",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001586"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_nonconservative_missense_codon_change_in_transcript"
+      "lbl" : "paralogous"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001726",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001705",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "H3K27Me2",
+          "val" : "H3K4me1",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K27 di-methylation site",
+          "val" : "H3K4 mono-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:28:14Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T01:45:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K27_dimethylation_site"
+      "lbl" : "H3K4_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000879",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000858",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence that contains the code for two gene products.",
+          "val" : "An attribute describing a kind of homology where divergence occurred after a speciation event.",
           "xrefs" : [ "SO:ke" ]
         },
         "basicPropertyValues" : [ {
@@ -22141,201 +26399,193 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dicistronic"
+      "lbl" : "orthologous"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001725",
+      "id" : "http://purl.obolibrary.org/obo/so#has_origin",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "has_origin"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00036",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001148"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001708",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "H3K4Me2",
+          "val" : "H2K27Me1",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K4 di-methylation site",
+          "val" : "H2K27 mono-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:03:15Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:31:54Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K4_dimethylation_site"
+      "lbl" : "H3K27_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000060",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001707",
       "meta" : {
         "definition" : {
-          "val" : "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing conservative missense codon change in transcript",
+          "val" : "H3K9Me3",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing conservative missense codon change in transcript",
+          "val" : "H3K9 tri-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001585"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:30:34Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_conservative_missense_codon_change_in_transcript"
+      "lbl" : "H3K9_trimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000878",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000855",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence that contains the code for one gene product.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "monocistronic"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000067",
-      "meta" : {
-        "definition" : {
-          "val" : "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide.",
+          "val" : "A homologous_region that is orthologous to another region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This term should be used in conjunction with the similarity relationships defined in SO." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Ortholog#Orthology"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing minus 1 frameshift",
+          "val" : "ortholog",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "minus 1 frameshift mutation",
+          "val" : "orthologue",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "orthologous region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001592"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_minus_1_frameshift"
+      "lbl" : "orthologous_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000873",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001702",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that is edited.",
+          "val" : "A histone modification where the modification is the acylation of the residue.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "edited transcript",
+          "val" : "histone acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "histone acetylation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:23:27Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edited_transcript"
+      "lbl" : "histone_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001720",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000041",
       "meta" : {
         "definition" : {
-          "val" : "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence.",
-          "xrefs" : [ "SO:ke", "http://en.wikipedia.org/wiki/Epigenetics" ]
+          "val" : "A chromosome structure variation whereby a transposition occurred within a chromosome.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "intrachromosomal transposition",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "epigenetically modified region",
+          "val" : "(Drosophila)Tp",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-27T12:02:29Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "epigenetically_modified_region"
+      "lbl" : "intrachromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000066",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000854",
       "meta" : {
         "definition" : {
-          "val" : "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide.",
+          "val" : "A homologous_region that is paralogous to another region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A term to be used in conjunction with the paralogous_to relationship." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Paralog#Paralogy"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing plus 1 frameshift mutation",
+          "val" : "paralogous region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "plus 1 frameshift mutation",
+          "val" : "paralog",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001594"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_plus_1_frameshift_mutation"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000872",
-      "meta" : {
-        "definition" : {
-          "val" : "An mRNA that is trans-spliced.",
-          "xrefs" : [ "SO:xp" ]
-        },
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "trans-spliced mRNA",
+          "val" : "paralogue",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22344,54 +26594,44 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trans_spliced_mRNA"
+      "lbl" : "paralogous_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000065",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000040",
       "meta" : {
         "definition" : {
-          "val" : "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.",
+          "val" : "A tandem duplication where the individual regions are not in the same orientation.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Frameshift_mutation"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "frameshift sequence variation",
+          "pred" : "hasExactSynonym",
+          "val" : "inverted tandem duplication",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "out of frame mutation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "frameshift mutation",
+          "val" : "mirror duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "frameshift_sequence_variation"
+      "lbl" : "inverted_tandem_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001722",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001701",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.",
+          "val" : "A histone modification site where the modification is the methylation of the residue.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K36<Me1",
+          "pred" : "hasExactSynonym",
+          "val" : "histone methylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K36 mono-methylation site",
+          "val" : "histone methylation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22402,182 +26642,138 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T10:46:32Z"
+          "val" : "2010-03-31T10:23:02Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K36_monomethylation_site"
+      "lbl" : "histone_methylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000875",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001704",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence that is bound by a protein.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bound by protein",
+          "val" : "H3K14ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H3K14 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:25:53Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bound_by_protein"
+      "lbl" : "H3K14_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000064",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000857",
       "meta" : {
         "definition" : {
-          "val" : "An umbrella term for terms describing an effect of a sequence variation on the frame of translation.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "Similarity due to common ancestry.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence variation affecting reading frame",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation affecting reading frame",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variation_affecting_reading_frame"
+      "lbl" : "homologous"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001721",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001703",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K27 acylation site",
+          "val" : "H3K9 acetylation site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K27Ac",
+          "pred" : "hasExactSynonym",
+          "val" : "H3K9ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T10:44:09Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:25:05Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K27_acylation_site"
+      "lbl" : "H3K9_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000874",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000856",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that has been edited by A to I substitution.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "edited transcript by A to I substitution",
+          "val" : "A region that is similar or identical across more than one species.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edited_transcript_by_A_to_I_substitution"
+      "lbl" : "conserved"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000049",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000045",
       "meta" : {
         "definition" : {
-          "val" : "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Ring_chromosome" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Ring_chromosome"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence_variant_causing_uncharacterised_change_in_transcript",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing partially characterised change in transcript",
+          "val" : "(Drosophila)R",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing uncharacterised change in transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence_variant_causing_partially_characterised_change_in_transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing uncharacterised change in transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation affecting transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing partially characterised change in transcript",
+          "val" : "(fungi)C",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variation affecting transcript",
+          "val" : "ring chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001576"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000177"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000179"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variation_affecting_transcript"
+      "lbl" : "ring_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000048",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000851",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A region of a CDS.",
+          "xrefs" : [ "SO:cb" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "reciprocal chromosomal translocation",
+          "val" : "CDS region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22586,36 +26782,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reciprocal_chromosomal_translocation"
+      "lbl" : "CDS_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000047",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000850",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal inversion that does not include the centromere.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A component of the five-prime long terminal repeat.",
+          "xrefs" : [ "PMID:8649407" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "paracentric inversion",
+          "val" : "5' long term repeat component",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "paracentric_inversion"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000871",
-      "meta" : {
-        "definition" : {
-          "val" : "An mRNA that is polyadenylated.",
-          "xrefs" : [ "SO:xp" ]
-        },
-        "synonyms" : [ {
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "polyadenylated mRNA",
+          "val" : "five prime LTR component",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22624,17 +26805,28 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polyadenylated_mRNA"
+      "lbl" : "five_prime_LTR_component"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000046",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000044",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal inversion that includes the centromere.",
+          "val" : "A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations.",
           "xrefs" : [ "FB:reference_manual" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Chromosomal_translocation"
+        } ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(fungi)T",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "pericentric inversion",
+          "val" : "chromosomal translocation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)T",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22643,17 +26835,28 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pericentric_inversion"
+      "lbl" : "chromosomal_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000870",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000853",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing transcript sequence that is created by splicing exons from diferent genes.",
+          "val" : "A region that is homologous to another region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Homology_(biology)"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "trans-spliced",
+          "val" : "homolog",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "homologue",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "homologous region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22662,83 +26865,97 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trans_spliced"
+      "lbl" : "homologous_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#guides",
+      "id" : "http://purl.obolibrary.org/obo/so#finished_by",
       "meta" : {
+        "definition" : {
+          "val" : "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary.",
+          "xrefs" : [ "PMID:20226267" ]
+        },
+        "comments" : [ "Example CDS finished_by stop_codon." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T02:27:24Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T01:45:45Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "PROPERTY",
-      "lbl" : "guides"
+      "lbl" : "finished_by"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001717",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000043",
       "meta" : {
         "definition" : {
-          "val" : "A histone modification site on H2B where ubiquitin may be added.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Robertsonian_translocation" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Robertsonian_fusion"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H2BUbiq",
+          "pred" : "hasExactSynonym",
+          "val" : "centric-fusion translocations",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Robertsonian fusion",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "whole-arm translocations",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T10:13:28Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2B_ubiquitination_site"
+      "lbl" : "Robertsonian_fusion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001716",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001700",
       "meta" : {
         "definition" : {
-          "val" : "A histone modification site where ubiquitin may be added.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation.",
+          "xrefs" : [ "http:en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "histone ubiquitination site",
+          "val" : "histone modification site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "histone modification",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T10:12:18Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:22:08Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histone_ubiqitination_site"
+      "lbl" : "histone_modification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000869",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000042",
       "meta" : {
         "definition" : {
-          "val" : "A frameshift caused by inserting two bases.",
+          "val" : "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plus 2 framshift",
+          "val" : "compound chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22747,75 +26964,56 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plus_2_framshift"
+      "lbl" : "compound_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001719",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000852",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of an exon.",
+          "xrefs" : [ "RSC:cb" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K23ac",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K23 acetylation site",
+          "val" : "exon region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T10:42:45Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K23_acetylation_site"
+      "lbl" : "exon_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001718",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000027",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "val" : "A transversion from guanine to thymine.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K18 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K18ac",
+          "val" : "G to T transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T10:39:35Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K18_acetylation_site"
+      "lbl" : "G_to_T_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000866",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000026",
       "meta" : {
         "definition" : {
-          "val" : "A frameshift caused by deleting one base.",
+          "val" : "A transversion from guanine to cytidine.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "minus 1 frameshift",
+          "val" : "G to C transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22824,45 +27022,37 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_1_frameshift"
+      "lbl" : "G_to_C_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001713",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000025",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "A transversion from adenine to thymine.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H4K20Me1",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "H4K20 mono-methylation site",
+          "val" : "A to T transversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:36:43Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4K20_monomethylation_site"
+      "lbl" : "A_to_T_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000865",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000024",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.",
+          "val" : "A transversion from adenine to cytidine.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Frameshift"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "A to C transversion",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -22870,122 +27060,147 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "frameshift"
+      "lbl" : "A_to_C_transversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001712",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000029",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "An incomplete chromosome.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Chromosomal_deletion"
+        } ],
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "chromosomal deletion",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "H3K79Me3",
+          "val" : "(bacteria)&ampDgr;",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(fungi)D",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)Df",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K79 tri-methylation site",
+          "val" : "deficiency",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:35:30Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K79_trimethylation_site"
+      "lbl" : "chromosomal_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001715",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000028",
       "meta" : {
         "definition" : {
-          "val" : "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.",
-          "xrefs" : [ "http://genesdev.cshlp.org/content/2/4/383.abstrac" ]
+          "val" : "A chromosomal structure variation within a single chromosome.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "interferon stimulated response element",
+          "val" : "intrachromosomal mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-05T11:15:08Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ISRE"
+      "lbl" : "intrachromosomal_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000868",
+      "id" : "http://purl.obolibrary.org/obo/BS_00041",
       "meta" : {
-        "definition" : {
-          "val" : "A frameshift caused by inserting one base.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "plus 1 frameshift",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001080"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00040",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001117"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#sequence_of",
+      "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "plus_1_frameshift"
+      "type" : "PROPERTY",
+      "lbl" : "sequence_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000050",
+      "id" : "http://purl.obolibrary.org/obo/BS_00042",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001111"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000848",
       "meta" : {
         "definition" : {
-          "val" : "No effect on the state of the RNA.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "The long terminal repeat found at the ends of the sequence to be inserted into the host genome.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing no change in transcript",
+          "pred" : "hasExactSynonym",
+          "val" : "LTR component",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing no change in transcript",
+          "val" : "long term repeat component",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_no_change_in_transcript"
+      "lbl" : "LTR_component"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000867",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000847",
       "meta" : {
         "definition" : {
-          "val" : "A frameshift caused by deleting two bases.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a tmRNA.",
+          "xrefs" : [ "SO:cb" ]
         },
+        "comments" : [ "This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "minus 2 frameshift",
+          "val" : "tmRNA region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -22994,248 +27209,214 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_2_frameshift"
+      "lbl" : "tmRNA_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001714",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000849",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "A component of the three-prime long terminal repeat.",
+          "xrefs" : [ "PMID:8649407" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK5 mono-methylation site",
+          "val" : "three prime LTR component",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3' long terminal repeat component",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:38:12Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2BK5_monomethylation_site"
+      "lbl" : "three_prime_LTR_component"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000056",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000030",
       "meta" : {
         "definition" : {
-          "val" : "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Chromosomal_inversion"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing amino acid coding codon change in transcript",
+          "val" : "chromosomal inversion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutaton causing amino acid coding codon change in transcript",
+          "val" : "(Drosophila)In",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0001606"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "hasRelatedSynonym",
+          "val" : "(fungi)In",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(bacteria)IN",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_amino_acid_coding_codon_change_in_transcript"
+      "lbl" : "chromosomal_inversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000862",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000844",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA that is capped.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A region of sequence which is a promoter for RNA polymerase II.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "capped mRNA",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "capped_mRNA"
+      "lbl" : "RNApol_II_promoter_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000055",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000843",
       "meta" : {
         "definition" : {
-          "val" : "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A region which is part of a bacterial RNA polymerase promoter.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing initiator codon change in transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing initiator codon change in transcript",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001582"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_initiator_codon_change_in_transcript"
+      "lbl" : "bacterial_RNApol_promoter_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000861",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000846",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript that is capped.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A region of sequence which is a promoter for RNA polymerase III type 2.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "capped primary transcript",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "capped_primary_transcript"
+      "lbl" : "RNApol_III_promoter_type_2_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000054",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000845",
       "meta" : {
         "definition" : {
-          "val" : "Any of the amino acid coding triplets of a gene are affected by the DNA mutation.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A region of sequence which is a promoter for RNA polymerase III type 1.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence variation affecting coding sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation affecting coding sequence",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001580"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variation_affecting_coding_sequence"
+      "lbl" : "RNApol_III_promoter_type_1_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001711",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000034",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000667"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000840",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "A region of a repeated sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A manufactured to group the parts of repeats, to give them an is_a path back to the root." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K79 di-methylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K79Me2",
+          "val" : "repeat component",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:34:39Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K79_dimethylation_site"
+      "lbl" : "repeat_component"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000864",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000033",
       "meta" : {
-        "definition" : {
-          "val" : "An attribute describing a sequence is representative of a class of similar sequences.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000159"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "exemplar"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001710",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000032",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
+          "val" : "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.",
+          "xrefs" : [ "http://varnomen.hgvs.org/recommendations/DNA/variant/delins/" ]
         },
+        "comments" : [ "Indels can have a different number of bases than the corresponding reference sequence. The term name was changed from indel to delins on 2/24/2019 to align with the HGVS nomenclature term for a deletion-insertion. Indel was causing confusion in the annotation community (github issue 445). The HGVS nomenclature definition of deletion-insertion (delins) is a sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution, inversion or conversion." ],
+        "xrefs" : [ {
+          "val" : "loinc:LA9659-9"
+        }, {
+          "val" : "http://en.wikipedia.org/wiki/Indel"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K79 mono-methylation site",
+          "val" : "deletion-insertion",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H3K79me1",
+          "pred" : "hasExactSynonym",
+          "val" : "indel",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-31T10:33:42Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K79_monomethylation_site"
+      "lbl" : "delins"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000863",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000842",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an mRNA feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a gene that has a specific function.",
+          "xrefs" : [ ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mRNA attribute",
+          "val" : "gene component region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -23244,42 +27425,38 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_attribute"
+      "lbl" : "gene_component_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001751",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000841",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A region within an intron.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A terms added to allow the parts of introns to have is_a paths to the root." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL6 acceptor site",
+          "val" : "spliceosomal intron region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:10:14Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL6_acceptor_site"
+      "lbl" : "spliceosomal_intron_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000420",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000031",
       "meta" : {
+        "definition" : {
+          "val" : "A chromosomal structure variation whereby more than one chromosome is involved.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5' TIR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five prime terminal inverted repeat",
+          "val" : "interchromosomal mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -23288,307 +27465,280 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_terminal_inverted_repeat"
+      "lbl" : "interchromosomal_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001750",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000880",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "An attribute describing a sequence that contains the code for more than one gene product.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "SL5 acceptor site",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:09:36Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL5_acceptor_site"
+      "lbl" : "polycistronic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000079",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000059",
       "meta" : {
+        "definition" : {
+          "val" : "The nucleotide change in the codon leads to a new codon coding for a new amino acid.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation affecting transcript sequence",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing missense codon change in transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variation affecting transcript sequence",
+          "val" : "sequence variant causing missense codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001583"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variation_affecting_transcript_sequence"
+      "lbl" : "sequence_variant_causing_missense_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000419",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000058",
       "meta" : {
         "definition" : {
-          "val" : "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.",
-          "xrefs" : [ "EBIBS:GAR", "SO:cb", "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A DNA point mutation that causes a substitution of an amino acid by an other.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "mature peptide",
+          "val" : "mutation causing non synonymous codon change in transcript",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "chain",
-          "xrefs" : [ "uniprot:feature_type" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:mat_peptide",
+          "val" : "non-synonymous codon change in transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "mature protein region",
+          "val" : "sequence variant causing non synonymous codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00149"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001583"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "mature_protein_region"
+      "lbl" : "sequence_variant_causing_non_synonymous_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000081",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000882",
       "meta" : {
         "definition" : {
-          "val" : "A mutation that alters the rate a which transcription of the sequence occurs.",
+          "val" : "An attribute describing the alteration of codon meaning.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting rate of transcription",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting rate of transcription",
+          "val" : "codon redefined",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001550"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_rate_of_transcription"
+      "lbl" : "codon_redefined"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000418",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000881",
       "meta" : {
         "definition" : {
-          "val" : "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Signal_peptide"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:sig_peptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "signal peptide coding sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "signal peptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "signal",
-          "xrefs" : [ "uniprot:feature_type" ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00159"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "signal_peptide"
+      "lbl" : "recoded"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000080",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000057",
       "meta" : {
+        "definition" : {
+          "val" : "The changed codon has the same translation product as the original codon.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variation increasing rate of transcription",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing synonymous codon change in transcript",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation increasing rate of transcription",
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing synonymous codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001819"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_increasing_rate_of_transcription"
+      "lbl" : "sequence_variant_causing_synonymous_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001749",
+      "id" : "http://purl.obolibrary.org/obo/BS_00012",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000417"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001728",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL4 acceptor site",
+          "val" : "H3K9 di-methylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "H3K9Me2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T11:08:19Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:08:47Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL4_acceptor_site"
+      "lbl" : "H3K9_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000085",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001727",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.",
+          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting level of transcript",
+          "val" : "H3K9Me1",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variation affecting level of transcript",
+          "val" : "H3K9 mono-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001540"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T11:06:17Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variation_affecting_level_of_transcript"
+      "lbl" : "H3K9_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000899",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001729",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a nuclear pseudogene of a mitochndrial gene.",
+          "val" : "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nuclear mitochondrial",
+          "val" : "H4K16 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H4K16ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T11:09:41Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclear_mitochondrial"
+      "lbl" : "H4K16_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001746",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000063",
       "meta" : {
         "definition" : {
-          "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.",
-          "xrefs" : [ "SO:bm" ]
+          "val" : "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "paternal uniparental disomy",
+          "val" : "sequence variant causing terminator codon change in transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing terminator codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001590"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T02:03:30Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "paternal_uniparental_disomy"
+      "lbl" : "sequence_variant_causing_terminator_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000415",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000877",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature that is invalidated due to polyA priming.",
+          "val" : "An attribute describing a situation where a gene may encode for more than 1 transcript.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "invalidated by genomic polyA primed cDNA",
+          "val" : "alternatively spliced",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -23597,46 +27747,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "invalidated_by_genomic_polyA_primed_cDNA"
+      "lbl" : "alternatively_spliced"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000084",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001724",
       "meta" : {
         "definition" : {
-          "val" : "Sequence variant decreases the stability (half-life) of the transcript.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant decreasing transcript stability",
+          "val" : "H3K36 tri-methylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation decreasing transcript stability",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "sequence_variant_decreasing_transcript_stability"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001745",
-      "meta" : {
-        "definition" : {
-          "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.",
-          "xrefs" : [ "SO:bm" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "maternal uniparental disomy",
+          "val" : "H3K36Me3",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -23647,21 +27772,21 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T02:03:01Z"
+          "val" : "2010-04-13T11:01:58Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "maternal_uniparental_disomy"
+      "lbl" : "H3K36_trimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000898",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000876",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is epigenetically modified.",
+          "val" : "An attribute describing a sequence that is bound by a nucleic acid.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "epigenetically modified gene",
+          "val" : "bound by nucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -23670,407 +27795,318 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "epigenetically_modified_gene"
+      "lbl" : "bound_by_nucleic_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000414",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001723",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature that is invalidated due to genomic contamination.",
+          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "invalidated by genomic contamination",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "invalidated_by_genomic_contamination"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000417",
-      "meta" : {
-        "definition" : {
-          "val" : "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.",
-          "xrefs" : [ "EBIBS:GAR" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "domain",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "polypeptide domain",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "structural domain",
+          "pred" : "hasRelatedSynonym",
+          "val" : "H3K36Me2",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide_structural_domain",
+          "val" : "H3K36 di-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001069"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00134"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00012"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T10:59:35Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_domain"
+      "lbl" : "H3K36_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000083",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000062",
       "meta" : {
         "definition" : {
-          "val" : "Sequence variant increases the stability (half-life) of the transcript.",
+          "val" : "The nucleotide change in the codon triplet creates a terminator codon.",
           "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant increasing transcript stability",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing nonsense codon change in transcript",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation increasing transcript stability",
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing nonsense codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001587"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_increasing_transcript_stability"
+      "lbl" : "sequence_variant_causing_nonsense_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001748",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000061",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing nonconservative missense codon change in transcript",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "SL3 acceptor site",
+          "val" : "sequence variant causing nonconservative missense codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T02:58:40Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001586"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "SL3_acceptor_site"
+      "lbl" : "sequence_variant_causing_nonconservative_missense_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001747",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001726",
       "meta" : {
         "definition" : {
-          "val" : "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "open chromatin region",
+          "val" : "H3K27 di-methylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "H3K27Me2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T01:45:41Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T02:21:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by John Calley 3125900."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "open_chromatin_region"
+      "lbl" : "H3K27_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000416",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000879",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature that is invalidated due to partial processing.",
+          "val" : "An attribute describing a sequence that contains the code for two gene products.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "invalidated by partial processing",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "invalidated_by_partial_processing"
+      "lbl" : "dicistronic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000082",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001725",
       "meta" : {
         "definition" : {
-          "val" : "Sequence variant affects the stability of the transcript.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting transcript stability",
+          "val" : "H3K4 di-methylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting transcript stability",
+          "val" : "H3K4Me2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T11:03:15Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001546"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence variant_affecting_transcript_stability"
+      "lbl" : "H3K4_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001742",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000878",
       "meta" : {
         "definition" : {
-          "val" : "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.",
+          "val" : "An attribute describing a sequence that contains the code for one gene product.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "gain",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "copy number gain",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T01:54:09Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "copy_number_gain"
+      "lbl" : "monocistronic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000089",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000060",
       "meta" : {
         "definition" : {
-          "val" : "The sequence variant at RNA level does not lead to any change in polypeptide.",
+          "val" : "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position.",
           "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing no change of translational product",
+          "val" : "sequence variant causing conservative missense codon change in transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing no change of translational product",
+          "val" : "mutation causing conservative missense codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term."
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001585"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_no_change_of_translational_product"
+      "lbl" : "sequence_variant_causing_conservative_missense_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000411",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001720",
       "meta" : {
         "definition" : {
-          "val" : "A region that rescues.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification.",
+          "xrefs" : [ "SO:ke", "http://en.wikipedia.org/wiki/Epigenetics" ]
         },
+        "comments" : [ "Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "rescue fragment",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "rescue segment",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "rescue region",
+          "val" : "epigenetically modified region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-27T12:02:29Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rescue_region"
+      "lbl" : "epigenetically_modified_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000895",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000067",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.",
+          "val" : "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silenced by DNA methylation",
+          "val" : "sequence variant causing minus 1 frameshift",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "minus 1 frameshift mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001592"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "silenced_by_DNA_methylation"
+      "lbl" : "sequence_variant_causing_minus_1_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000410",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000873",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.",
+          "val" : "A transcript that is edited.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "protein binding site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:protein_bind",
+          "val" : "edited transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "See GO:0042277 : peptide binding."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "protein_binding_site"
+      "lbl" : "edited_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000088",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000066",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant causing a change in primary translation product of a transcript.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence_variant_causing_uncharacterised_change_of_translational_product",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing uncharacterised change of translational product",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing uncharacterised change of translational product",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing partially characterised change of translational product",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence_variant_causing_partially_characterised_change_of_translational_product",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing partially characterised change of translational product",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting translational product",
+          "val" : "plus 1 frameshift mutation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting translational product",
+          "val" : "sequence variant causing plus 1 frameshift mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001553"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "val" : "SO:0001594"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000090"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000091"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_translational_product"
+      "lbl" : "sequence_variant_causing_plus_1_frameshift_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000894",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000872",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An mRNA that is trans-spliced.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silenced by DNA modification",
+          "val" : "trans-spliced mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -24079,128 +28115,121 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silenced_by_DNA_modification"
+      "lbl" : "trans_spliced_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001741",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000875",
       "meta" : {
         "definition" : {
-          "val" : "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.",
-          "xrefs" : [ "SO:hd" ]
+          "val" : "An attribute describing a sequence that is bound by a protein.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pseudogenic gene segment",
+          "val" : "bound by protein",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "batchelorc"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-15T05:07:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudogenic_gene_segment"
+      "lbl" : "bound_by_protein"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000413",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000065",
       "meta" : {
         "definition" : {
-          "val" : "A region where the sequence differs from that of a specified sequence.",
+          "val" : "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Frameshift_mutation"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence difference",
+          "pred" : "hasRelatedSynonym",
+          "val" : "frameshift sequence variation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:misc_difference",
+          "val" : "frameshift mutation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "out of frame mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_difference"
+      "lbl" : "frameshift_sequence_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001744",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001722",
       "meta" : {
         "definition" : {
-          "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.",
-          "xrefs" : [ "SO:BM" ]
+          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
-        "xrefs" : [ {
-          "val" : "http:http://en.wikipedia.org/wiki/Uniparental_disomy"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "uniparental disomy",
+          "val" : "H3K36 mono-methylation site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "UPD",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "H3K36Me1",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T10:46:32Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T02:01:05Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "UPD"
+      "lbl" : "H3K36_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000087",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000064",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An umbrella term for terms describing an effect of a sequence variation on the frame of translation.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variation increasing level of transcript",
+          "pred" : "hasRelatedSynonym",
+          "val" : "sequence variation affecting reading frame",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "mutation increasing level of transcript",
+          "val" : "mutation affecting reading frame",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variation_increasing_level_of_transcript"
+      "lbl" : "sequence_variation_affecting_reading_frame"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000897",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000874",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is allelically_excluded.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A transcript that has been edited by A to I substitution.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "allelically excluded gene",
+          "val" : "edited transcript by A to I substitution",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -24209,118 +28238,124 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "allelically_excluded_gene"
+      "lbl" : "edited_transcript_by_A_to_I_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001743",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001721",
       "meta" : {
         "definition" : {
-          "val" : "A sequence alteration whereby the copy number of a given region is less than the reference sequence.",
+          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "copy number loss",
+          "val" : "H3K27 acylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "loss",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
+          "val" : "H3K27Ac",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T01:55:02Z"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "copy_number_loss"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000896",
-      "meta" : {
-        "definition" : {
-          "val" : "A gene that is translationally regulated.",
-          "xrefs" : [ "SO:xp" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "translationally regulated gene",
-          "xrefs" : [ ]
+          "val" : "2010-04-13T10:44:09Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "translationally_regulated_gene"
+      "lbl" : "H3K27_acylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000412",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000049",
       "meta" : {
         "definition" : {
-          "val" : "A region of polynucleotide sequence produced by digestion with a restriction endonuclease.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Restriction_fragment"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "restriction fragment",
+          "val" : "sequence variant causing uncharacterised change in transcript",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing partially characterised change in transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mutation affecting transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing uncharacterised change in transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variation affecting transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence_variant_causing_partially_characterised_change_in_transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing partially characterised change in transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence_variant_causing_uncharacterised_change_in_transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001576"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000177"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000179"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "restriction_fragment"
+      "lbl" : "sequence_variation_affecting_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000086",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000048",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence variation decreasing level of transcript",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "mutation decreasing level of transcript",
+          "val" : "reciprocal chromosomal translocation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variation_decreasing_level_of_transcript"
+      "lbl" : "reciprocal_chromosomal_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000891",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000047",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is negatively autoreguated.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A chromosomal inversion that does not include the centromere.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "negatively autoregulated gene",
+          "val" : "paracentric inversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -24329,17 +28364,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "negatively_autoregulated_gene"
+      "lbl" : "paracentric_inversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000890",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000871",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is post translationally regulated.",
+          "val" : "An mRNA that is polyadenylated.",
           "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "post translationally regulated gene",
+          "val" : "polyadenylated mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -24348,263 +28383,224 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "post_translationally_regulated_gene"
+      "lbl" : "polyadenylated_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001740",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000046",
       "meta" : {
         "definition" : {
-          "val" : "A gene with a translational start codon of CUG.",
-          "xrefs" : [ "SO:mc" ]
+          "val" : "A chromosomal inversion that includes the centromere.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with start codon CUG",
+          "val" : "pericentric inversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-01-10T01:32:35Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by flybase, Dec 2010."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_start_codon_CUG"
+      "lbl" : "pericentric_inversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000069",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000870",
       "meta" : {
         "definition" : {
-          "val" : "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides.",
+          "val" : "An attribute describing transcript sequence that is created by splicing exons from diferent genes.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "minus 2 frameshift mutation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing minus 2 frameshift",
+          "val" : "trans-spliced",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001593"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_minus_2_frameshift"
+      "lbl" : "trans_spliced"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000893",
+      "id" : "http://purl.obolibrary.org/obo/so#guides",
       "meta" : {
-        "definition" : {
-          "val" : "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Silenced"
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-08-19T02:27:24Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "silenced"
+      "type" : "PROPERTY",
+      "lbl" : "guides"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000068",
+      "id" : "http://purl.obolibrary.org/obo/BS_00027",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001092"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001717",
       "meta" : {
         "definition" : {
-          "val" : "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides.",
+          "val" : "A histone modification site on H2B where ubiquitin may be added.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "plus 2 frameshift mutation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing plus 2 frameshift",
+          "pred" : "hasRelatedSynonym",
+          "val" : "H2BUbiq",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001595"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T10:13:28Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_plus_2_frameshift"
+      "lbl" : "H2B_ubiquitination_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000892",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001716",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is positively autoregulated.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A histone modification site where ubiquitin may be added.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "positively autoregulated gene",
+          "pred" : "hasRelatedSynonym",
+          "val" : "histone ubiquitination site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T10:12:18Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "positively_autoregulated_gene"
+      "lbl" : "histone_ubiqitination_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000408",
+      "id" : "http://purl.obolibrary.org/obo/BS_00026",
       "meta" : {
-        "definition" : {
-          "val" : "The interbase position where something (eg an aberration) occurred.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001104"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "site"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001739",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000869",
       "meta" : {
         "definition" : {
-          "val" : "A gene with a start codon other than AUG.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A frameshift caused by inserting two bases.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with non canonical start codon",
+          "val" : "plus 2 framshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-01-10T01:30:31Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by flybase, Dec 2010."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_non_canonical_start_codon"
+      "lbl" : "plus_2_framshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000070",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001719",
       "meta" : {
         "definition" : {
-          "val" : "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting transcript processing",
+          "pred" : "hasExactSynonym",
+          "val" : "H3K23 acetylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting transcript processing",
+          "val" : "H3K23ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001543"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T10:42:45Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_transcript_processing"
+      "lbl" : "H3K23_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001738",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001718",
       "meta" : {
         "definition" : {
-          "val" : "A region of the H4 histone whereby multiple lysines are acylated.",
+          "val" : "A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H4K acylation region",
+          "val" : "H3K18 acetylation site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H4KAc",
+          "pred" : "hasExactSynonym",
+          "val" : "H3K18ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T02:00:06Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2010-04-13T10:39:35Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4K_acylation_region"
+      "lbl" : "H3K18_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000407",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000866",
       "meta" : {
         "definition" : {
-          "val" : "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome.",
+          "val" : "A frameshift caused by deleting one base.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/18S_ribosomal_RNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA 18S",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "18S rRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "18S ribosomal RNA",
+          "val" : "minus 1 frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -24613,59 +28609,45 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_18S"
+      "lbl" : "minus_1_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000409",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001713",
       "meta" : {
         "definition" : {
-          "val" : "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.",
-          "xrefs" : [ "EBIBS:GAR", "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Binding_site"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "binding_or_interaction_site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "binding site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:misc_binding",
+          "val" : "H4K20 mono-methylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "site",
+          "val" : "H4K20Me1",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:36:43Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00033"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "See GO:0005488 : binding."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "binding_site"
+      "lbl" : "H4K20_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000888",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000865",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is maternally_imprinted.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "maternally imprinted gene",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Frameshift"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -24673,287 +28655,262 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "maternally_imprinted_gene"
+      "lbl" : "frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000404",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001712",
       "meta" : {
         "definition" : {
-          "val" : "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006" ]
+          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Vault_RNA"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "vault RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "H3K79Me3",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:vault_RNA",
+          "val" : "H3K79 tri-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:35:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vault_RNA"
+      "lbl" : "H3K79_trimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000074",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000050",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant causing a new (functional) splice site.",
+          "val" : "No effect on the state of the RNA.",
           "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "cryptic splice activator sequence variant",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing cryptic splice activator",
+          "val" : "mutation causing no change in transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing cryptic splice activator",
+          "val" : "sequence variant causing no change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001569"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_cryptic_splice_activation"
+      "lbl" : "sequence_variant_causing_no_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001735",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001715",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding.",
+          "xrefs" : [ "http://genesdev.cshlp.org/content/2/4/383.abstrac" ]
         },
+        "comments" : [ "Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. Moved from is_a SO:0001055 transcriptional_cis_regulatory_region to SO:0000235 TF_binding_site after Colin Logie pointed out that this is a consensus sequence where transcription factors bind, GREEKC Jan 21, 2021." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K79 methylation site",
+          "val" : "interferon stimulated response element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:29:16Z"
+          "val" : "2010-04-05T11:15:08Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K79_methylation_site"
+      "lbl" : "ISRE"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000403",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000868",
       "meta" : {
         "definition" : {
-          "val" : "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.",
-          "xrefs" : [ "PMID:2551119", "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016" ]
+          "val" : "A frameshift caused by inserting one base.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snoRNA U14",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small nucleolar RNA U14",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U14 snoRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U14 small nucleolar RNA",
+          "val" : "plus 1 frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0005839"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U14_snoRNA"
+      "lbl" : "plus_1_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001734",
+      "id" : "http://purl.obolibrary.org/obo/BS_00029",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001091"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000867",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.",
+          "val" : "A frameshift caused by deleting two bases.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K4 methylation site",
+          "val" : "minus 2 frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:28:14Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K4_methylation_site"
+      "lbl" : "minus_2_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000073",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001714",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_variant_effect that changes the splice acceptor sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting splicing",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "splice acceptor mutation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence variant affecting splice acceptor",
+          "val" : "H2BK5 mono-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:38:12Z"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001574"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_splice_acceptor"
+      "lbl" : "H2BK5_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000887",
+      "id" : "http://purl.obolibrary.org/obo/BS_00028",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001088"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000056",
       "meta" : {
         "definition" : {
-          "val" : "Recoding by frameshifting a particular site.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutaton causing amino acid coding codon change in transcript",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "translationally frameshifted",
+          "val" : "sequence variant causing amino acid coding codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0001606"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "translationally_frameshifted"
+      "lbl" : "sequence_variant_causing_amino_acid_coding_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000072",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000862",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_variant_effect that changes the splice donor sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An mRNA that is capped.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice donor mutation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting splice donor",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence variant affecting splice donor",
+          "val" : "capped mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001575"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_splice_donor"
+      "lbl" : "capped_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001737",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000055",
       "meta" : {
         "definition" : {
-          "val" : "A histone modification, whereby the histone protein is acylated at multiple sites in a region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "histone acylation region",
+          "val" : "mutation causing initiator codon change in transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing initiator codon change in transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T01:58:21Z"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001582"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "histone_acylation_region"
+      "lbl" : "sequence_variant_causing_initiator_codon_change_in_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000406",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000861",
       "meta" : {
         "definition" : {
-          "val" : "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.",
-          "xrefs" : [ "PMID:1899376", "PMID:7823908" ]
+          "val" : "A primary transcript that is capped.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Twintron"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "capped primary transcript",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -24961,229 +28918,210 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "twintron"
+      "lbl" : "capped_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000889",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001711",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is paternally imprinted.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "H3K79Me2",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "paternally imprinted gene",
+          "val" : "H3K79 di-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:34:39Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "paternally_imprinted_gene"
+      "lbl" : "H3K79_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001736",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000864",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated.",
+          "val" : "An attribute describing a sequence is representative of a class of similar sequences.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K9 methylation site",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:31:37Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K9_methylation_site"
+      "lbl" : "exemplar"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000405",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000054",
       "meta" : {
         "definition" : {
-          "val" : "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019" ]
+          "val" : "Any of the amino acid coding triplets of a gene are affected by the DNA mutation.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Y_RNA"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Y RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "sequence variation affecting coding sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:Y_RNA",
+          "val" : "mutation affecting coding sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001580"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "Y_RNA"
+      "lbl" : "sequence_variation_affecting_coding_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000071",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000863",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An attribute describing an mRNA feature.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting splicing",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting splicing",
+          "val" : "mRNA attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001568"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_splicing"
+      "lbl" : "mRNA_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000078",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001710",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variation that decreases the rate a which transcription of the sequence occurs.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Histone" ]
         },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation decreasing rate of transcription",
+          "val" : "H3K79me1",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variation decreasing rate of transcription",
+          "val" : "H3K79 mono-methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-31T10:33:42Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_decreasing_rate_of_transcription"
+      "lbl" : "H3K79_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000884",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001751",
       "meta" : {
         "definition" : {
-          "val" : "A stop codon redefined to be the new amino acid, pyrrolysine.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "stop codon redefined as pyrrolysine",
+          "val" : "SL6 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T03:10:14Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stop_codon_redefined_as_pyrrolysine"
+      "lbl" : "SL6_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001731",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000420",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated.",
-          "xrefs" : [ "SO:KE" ]
+          "val" : "An inverted repeat (SO:0000294) occurring at the 5-prime termini of a DNA transposon.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H4K8ac",
+          "val" : "5' TIR",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H4K8 acetylation site",
+          "val" : "five prime terminal inverted repeat",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:14:24Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4K8_acetylation_site"
+      "lbl" : "five_prime_terminal_inverted_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000400",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000079",
       "meta" : {
-        "definition" : {
-          "val" : "An attribute describes a quality of sequence.",
-          "xrefs" : [ "SO:ke" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence attribute",
+          "val" : "sequence variation affecting transcript sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mutation affecting transcript sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_attribute"
+      "lbl" : "sequence_variation_affecting_transcript_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001730",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001750",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H4K5 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H4K5ac",
+          "val" : "SL5 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:13:00Z"
+          "val" : "2011-02-28T03:09:36Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -25193,216 +29131,258 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4K5_acetylation_site"
+      "lbl" : "SL5_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000883",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000419",
       "meta" : {
         "definition" : {
-          "val" : "A stop codon redefined to be a new amino acid.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide.",
+          "xrefs" : [ "EBIBS:GAR", "SO:cb", "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mature peptide",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "stop codon read through",
+          "val" : "mature protein region",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "stop codon readthrough",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:mat_peptide",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "chain",
+          "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00149"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stop_codon_read_through"
+      "lbl" : "mature_protein_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001733",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000081",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.",
+          "val" : "A mutation that alters the rate a which transcription of the sequence occurs.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting rate of transcription",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K36 methylation site",
+          "val" : "sequence variant affecting rate of transcription",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:27:28Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001550"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "H3K36_methylation_site"
+      "lbl" : "sequence_variant_affecting_rate_of_transcription"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000886",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001749",
       "meta" : {
         "definition" : {
-          "val" : "Recoded mRNA where a block of nucleotides is not translated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "recoded by translational bypass",
+          "val" : "SL4 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T03:08:47Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recoded_by_translational_bypass"
+      "lbl" : "SL4_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000076",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000080",
       "meta" : {
-        "definition" : {
-          "val" : "Mutation affects the process of transcription, its initiation, progression or termination.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting transcription",
+          "val" : "sequence variation increasing rate of transcription",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting transcription",
+          "val" : "mutation increasing rate of transcription",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001549"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_transcription"
+      "lbl" : "sequence_variant_increasing_rate_of_transcription"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000402",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000418",
       "meta" : {
+        "definition" : {
+          "val" : "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
+        },
+        "comments" : [ "Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Signal_peptide"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "signal peptide coding sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "signal",
+          "xrefs" : [ "uniprot:feature_type" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "signal peptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:sig_peptide",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00159"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "enhancer_attribute"
+      "lbl" : "signal_peptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000885",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000085",
       "meta" : {
         "definition" : {
-          "val" : "A stop codon redefined to be the new amino acid, selenocysteine.",
+          "val" : "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting level of transcript",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "stop codon redefined as selenocysteine",
+          "val" : "sequence variation affecting level of transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001540"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "stop_codon_redefined_as_selenocysteine"
+      "lbl" : "sequence_variation_affecting_level_of_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001732",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000899",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.",
+          "val" : "An attribute describing a nuclear pseudogene of a mitochndrial gene.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K27 methylation site",
+          "val" : "nuclear mitochondrial",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-13T11:26:22Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "H3K27_methylation_site"
+      "lbl" : "nuclear_mitochondrial"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000075",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000415",
       "meta" : {
         "definition" : {
-          "val" : "Sequence variant affects the editing of the transcript.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "An attribute to describe a feature that is invalidated due to polyA priming.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting editing",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting editing",
+          "val" : "invalidated by genomic polyA primed cDNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001544"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_editing"
+      "lbl" : "invalidated_by_genomic_polyA_primed_cDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000401",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001746",
       "meta" : {
+        "definition" : {
+          "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother.",
+          "xrefs" : [ "SO:bm" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene attribute",
+          "val" : "paternal uniparental disomy",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T02:03:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_attribute"
+      "lbl" : "paternal_uniparental_disomy"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001771",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001745",
       "meta" : {
+        "definition" : {
+          "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father.",
+          "xrefs" : [ "SO:bm" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "disease associated variant",
+          "val" : "maternal uniparental disomy",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -25413,344 +29393,360 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:05:16Z"
+          "val" : "2011-02-28T02:03:01Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "disease_associated_variant"
+      "lbl" : "maternal_uniparental_disomy"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000440",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000084",
       "meta" : {
         "definition" : {
-          "val" : "A replicon that has been modified to act as a vector for foreign sequence.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "Sequence variant decreases the stability (half-life) of the transcript.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Vector_(molecular_biology)"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vector",
+          "val" : "sequence variant decreasing transcript stability",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "vector replicon",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation decreasing transcript stability",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "vector_replicon"
+      "lbl" : "sequence_variant_decreasing_transcript_stability"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001770",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000898",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is epigenetically modified.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "benign variant",
+          "val" : "epigenetically modified gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:55:40Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "benign_variant"
+      "lbl" : "epigenetically_modified_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001773",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000414",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute to describe a feature that is invalidated due to genomic contamination.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lethal variant",
+          "val" : "invalidated by genomic contamination",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:06:22Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lethal_variant"
+      "lbl" : "invalidated_by_genomic_contamination"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000442",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000083",
       "meta" : {
         "definition" : {
-          "val" : "A double stranded oligonucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Sequence variant increases the stability (half-life) of the transcript.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "ds-oligonucleotide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "double stranded oligonucleotide",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation increasing transcript stability",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ds oligo",
+          "val" : "sequence variant increasing transcript stability",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "ds_oligo"
+      "lbl" : "sequence_variant_increasing_transcript_stability"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000441",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000417",
       "meta" : {
         "definition" : {
-          "val" : "A single stranded oligonucleotide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "single stranded oligonucleotide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ss oligo",
+          "val" : "polypeptide domain",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ss oligonucleotide",
-          "xrefs" : [ ]
+          "pred" : "hasBroadSynonym",
+          "val" : "structural domain",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "single strand oligonucleotide",
-          "xrefs" : [ ]
+          "val" : "polypeptide_structural_domain",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "single strand oligo",
-          "xrefs" : [ ]
+          "pred" : "hasBroadSynonym",
+          "val" : "domain",
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00012"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001069"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00134"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ss_oligo"
+      "lbl" : "polypeptide_domain"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001772",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001748",
       "meta" : {
+        "definition" : {
+          "val" : "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "disease causing variant",
+          "val" : "SL3 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:05:46Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T02:58:40Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "disease_causing_variant"
+      "lbl" : "SL3_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001768",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000416",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute to describe a feature that is invalidated due to partial processing.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "fixed variant",
+          "val" : "invalidated by partial processing",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:50:53Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "fixed_variant"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000437",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "assortment_derived_duplication"
+      "lbl" : "invalidated_by_partial_processing"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001767",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001747",
       "meta" : {
+        "definition" : {
+          "val" : "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA.",
+          "xrefs" : [ "SO:cb" ]
+        },
+        "comments" : [ "Requested by John Calley 3125900." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "common variant",
+          "val" : "open chromatin region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:50:36Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T02:21:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "common_variant"
+      "lbl" : "open_chromatin_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000436",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000082",
       "meta" : {
         "definition" : {
-          "val" : "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "Sequence variant affects the stability of the transcript.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "autonomously replicating sequence",
+          "val" : "sequence variant affecting transcript stability",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting transcript stability",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001546"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "ARS"
+      "lbl" : "sequence variant_affecting_transcript_stability"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000439",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001742",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inverted ring chromosome",
+          "val" : "copy number gain",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "gain",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbvar"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T01:54:09Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inverted_ring_chromosome"
+      "lbl" : "copy_number_gain"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001769",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000411",
       "meta" : {
         "definition" : {
-          "val" : "A quality inhering in a variant by virtue of its phenotype.",
-          "xrefs" : [ "PMID:17597783", "SO:ke" ]
+          "val" : "A region that rescues.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "rescue segment",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "variant phenotype",
+          "val" : "rescue region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "rescue fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:53:15Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "variant_phenotype"
+      "lbl" : "rescue_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000438",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000089",
       "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+        "definition" : {
+          "val" : "The sequence variant at RNA level does not lead to any change in polypeptide.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term." ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing no change of translational product",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing no change of translational product",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "gene_not_polyadenylated"
+      "lbl" : "sequence_variant_causing_no_change_of_translational_product"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001764",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000895",
       "meta" : {
         "definition" : {
-          "val" : "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.",
+          "val" : "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unique variant",
+          "val" : "silenced by DNA methylation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:47:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unique_variant"
+      "lbl" : "silenced_by_DNA_methylation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000433",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000410",
       "meta" : {
         "definition" : {
-          "val" : "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.",
+          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "See GO:0042277 : peptide binding." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:non_ltr_retrotransposon_polymeric_tract",
+          "val" : "INSDC_feature:protein_bind",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non LTR retrotransposon polymeric tract",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "val" : "protein binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -25759,86 +29755,124 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_LTR_retrotransposon_polymeric_tract"
+      "lbl" : "protein_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000432",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000088",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant causing a change in primary translation product of a transcript.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U5 3' long terminal repeat region",
+          "val" : "sequence_variant_causing_uncharacterised_change_of_translational_product",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U5 three prime LTR region",
+          "val" : "sequence variant affecting translational product",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing partially characterised change of translational product",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting translational product",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing partially characterised change of translational product",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing uncharacterised change of translational product",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing uncharacterised change of translational product",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence_variant_causing_partially_characterised_change_of_translational_product",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000090"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000091"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001553"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "U5_three_prime_LTR_region"
+      "lbl" : "sequence_variant_affecting_translational_product"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001763",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001741",
       "meta" : {
         "definition" : {
-          "val" : "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.",
-          "xrefs" : [ "PMID:17597783", "SO:ke" ]
+          "val" : "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product.",
+          "xrefs" : [ "SO:hd" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "variant frequency",
+          "val" : "pseudogenic gene segment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:44:39Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "batchelorc"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-15T05:07:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "variant_frequency"
+      "lbl" : "pseudogenic_gene_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001766",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000894",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polymorphic variant",
+          "val" : "silenced by DNA modification",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:48:51Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polymorphic_variant"
+      "lbl" : "silenced_by_DNA_modification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000435",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000413",
       "meta" : {
         "definition" : {
-          "val" : "A polypurine tract within an LTR_retrotransposon.",
+          "val" : "A region where the sequence differs from that of a specified sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "LTR retrotransposon poly purine tract",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:misc_difference",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "RR tract",
+          "val" : "sequence difference",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -25847,146 +29881,155 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RR_tract"
+      "lbl" : "sequence_difference"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000434",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001744",
       "meta" : {
         "definition" : {
-          "val" : "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.",
-          "xrefs" : [ "http://www.koko.gov.my/CocoaBioTech/Glossaryt.html" ]
+          "val" : "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent.",
+          "xrefs" : [ "SO:BM" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
+        "xrefs" : [ {
+          "val" : "http:http://en.wikipedia.org/wiki/Uniparental_disomy"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "target site duplication",
+          "val" : "uniparental disomy",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "UPD",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbvar"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T02:01:05Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "target_site_duplication"
+      "lbl" : "UPD"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001765",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000897",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is allelically_excluded.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rare variant",
+          "val" : "allelically excluded gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:48:29Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rare_variant"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#BS",
-      "type" : "PROPERTY",
-      "lbl" : "biosapiens"
+      "lbl" : "allelically_excluded_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001760",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000087",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "SO:ke" ]
+          "val" : "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unprocessed pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "non processed pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "unprocessed_pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:gene",
+          "val" : "mutation increasing level of transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:unprocessed",
+          "val" : "sequence variation increasing level of transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-09T10:54:47Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "non_processed_pseudogene"
+      "lbl" : "sequence_variation_increasing_level_of_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000431",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000086",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "U3 three prime LTR region",
+          "pred" : "hasRelatedSynonym",
+          "val" : "sequence variation decreasing level of transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U3 3' long terminal repeat region",
+          "val" : "mutation decreasing level of transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "U3_three_prime_LTR_region"
+      "lbl" : "sequence_variation_decreasing_level_of_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001762",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001743",
       "meta" : {
         "definition" : {
-          "val" : "A quality inhering in a variant by virtue of its origin.",
-          "xrefs" : [ "PMID:17597783", "SO:ke" ]
+          "val" : "A sequence alteration whereby the copy number of a given region is less than the reference sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "loss",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbvar"
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "variant origin",
+          "val" : "copy number loss",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T01:55:02Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:42:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "variant_origin"
+      "lbl" : "copy_number_loss"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000430",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000412",
       "meta" : {
+        "definition" : {
+          "val" : "A region of polynucleotide sequence produced by digestion with a restriction endonuclease.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Restriction_fragment"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "R three prime LTR region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "R 3' long terminal repeat region",
+          "val" : "restriction fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -25995,65 +30038,36 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "R_three_prime_LTR_region"
+      "lbl" : "restriction_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001761",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000896",
       "meta" : {
         "definition" : {
-          "val" : "A dependent entity that inheres in a bearer, a sequence variant.",
-          "xrefs" : [ "PMID:17597783", "SO:ke" ]
+          "val" : "A gene that is translationally regulated.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "variant quality",
+          "val" : "translationally regulated gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T03:40:35Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "variant_quality"
+      "lbl" : "translationally_regulated_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#transcribed_to",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000891",
       "meta" : {
         "definition" : {
-          "val" : "Inverse of transcribed_from.",
-          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
+          "val" : "A gene that is negatively autoreguated.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T12:08:24Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: gene transcribed_to primary_transcript."
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "transcribed_to"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000429",
-      "meta" : {
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U3 5' long term repeat region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U3 five prime LTR region",
+          "val" : "negatively autoregulated gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26062,47 +30076,63 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U3_five_prime_LTR_region"
+      "lbl" : "negatively_autoregulated_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001757",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000890",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A gene that is post translationally regulated.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL12 acceptor site",
+          "val" : "post translationally regulated gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:17:23Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL12_acceptor_site"
+      "lbl" : "post_translationally_regulated_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000426",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000069",
       "meta" : {
+        "definition" : {
+          "val" : "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime LTR",
+          "val" : "sequence variant causing minus 2 frameshift",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "3' long terminal repeat",
+          "val" : "minus 2 frameshift mutation",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001593"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "3' LTR",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_variant_causing_minus_2_frameshift"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000893",
+      "meta" : {
+        "definition" : {
+          "val" : "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Silenced"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -26110,46 +30140,43 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_LTR"
+      "lbl" : "silenced"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001756",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001740",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A gene with a translational start codon of CUG.",
+          "xrefs" : [ "SO:mc" ]
         },
+        "comments" : [ "Requested by flybase, Dec 2010." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL11 acceptor site",
+          "val" : "gene with start codon CUG",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:16:54Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-01-10T01:32:35Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL11_acceptor_site"
+      "lbl" : "gene_with_start_codon_CUG"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000425",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000892",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is positively autoregulated.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime LTR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5' LTR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5' long terminal repeat",
+          "val" : "positively autoregulated gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26158,57 +30185,127 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_LTR"
+      "lbl" : "positively_autoregulated_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001759",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000068",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "SO:ke", "http://en.wikipedia.org/wiki/Pseudogene" ]
+          "val" : "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:unitary",
+          "val" : "plus 2 frameshift mutation",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "disabled gene",
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing plus 2 frameshift",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:gene",
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001595"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_variant_causing_plus_2_frameshift"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000070",
+      "meta" : {
+        "definition" : {
+          "val" : "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant affecting transcript processing",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "unitary pseudogene",
+          "val" : "mutation affecting transcript processing",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-09T10:04:04Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates."
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001543"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_variant_affecting_transcript_processing"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001739",
+      "meta" : {
+        "definition" : {
+          "val" : "A gene with a start codon other than AUG.",
+          "xrefs" : [ "SO:xp" ]
+        },
+        "comments" : [ "Requested by flybase, Dec 2010." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "gene with non canonical start codon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-01-10T01:30:31Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unitary_pseudogene"
+      "lbl" : "gene_with_non_canonical_start_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000428",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000408",
+      "meta" : {
+        "definition" : {
+          "val" : "The interbase position where something (eg an aberration) occurred.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000407",
       "meta" : {
+        "definition" : {
+          "val" : "Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Renamed to cytosolic_18S_rRNA from rRNA_18S on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/18S_ribosomal_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U5 5' long terminal repeat region",
+          "val" : "cytosolic rRNA 18S",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U5 five prime LTR region",
+          "val" : "cytosolic 18S ribosomal RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 18S rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26217,130 +30314,186 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U5_five_prime_LTR_region"
+      "lbl" : "cytosolic_18S_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001758",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001738",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Pseudogene" ]
+          "val" : "A region of the H4 histone whereby multiple lysines are acylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "H4K acylation region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "duplicated pseudogene",
+          "val" : "H4KAc",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T02:00:06Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-09T09:58:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "duplicated_pseudogene"
+      "lbl" : "H4K_acylation_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000427",
+      "id" : "http://purl.obolibrary.org/obo/BS_00003",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001078"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000409",
       "meta" : {
+        "definition" : {
+          "val" : "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids.",
+          "xrefs" : [ "EBIBS:GAR", "SO:ke" ]
+        },
+        "comments" : [ "See GO:0005488 : binding." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Binding_site"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "R 5' long term repeat region",
+          "val" : "binding site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "R five prime LTR region",
+          "val" : "INSDC_feature:misc_binding",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "binding_or_interaction_site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00033"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "R_five_prime_LTR_region"
+      "lbl" : "binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001753",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001735",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL8 acceptor site",
+          "val" : "H3K79 methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:15:26Z"
+          "val" : "2010-04-13T11:29:16Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL8_acceptor_site"
+      "lbl" : "H3K79_methylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000422",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000074",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant causing a new (functional) splice site.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "comments" : [ "A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U5 long terminal repeat region",
+          "val" : "sequence variant causing cryptic splice activator",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing cryptic splice activator",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U5 LTR region",
+          "val" : "cryptic splice activator sequence variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001569"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "U5_LTR_region"
+      "lbl" : "sequence_variant_causing_cryptic_splice_activation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001752",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000404",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Vault_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL37 acceptor site",
+          "val" : "INSDC_qualifier:vault_RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "vault RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:13:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL7_acceptor_site"
+      "lbl" : "vault_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000421",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000888",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is maternally_imprinted.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime terminal inverted repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "3' TIR",
+          "val" : "maternally imprinted gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26349,42 +30502,49 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_terminal_inverted_repeat"
+      "lbl" : "maternally_imprinted_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001755",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000073",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A sequence_variant_effect that changes the splice acceptor sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL10 acceptor site",
+          "val" : "splice acceptor mutation",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:16:31Z"
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting splicing",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "sequence variant affecting splice acceptor",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001574"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "SL10_acceptor_site"
+      "lbl" : "sequence_variant_affecting_splice_acceptor"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000424",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000887",
       "meta" : {
+        "definition" : {
+          "val" : "Recoding by frameshifting a particular site.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U3 long terminal repeat region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U3 LTR region",
+          "val" : "translationally frameshifted",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26393,22 +30553,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U3_LTR_region"
+      "lbl" : "translationally_frameshifted"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001754",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001734",
       "meta" : {
         "definition" : {
-          "val" : "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL9 acceptor site",
+          "val" : "H3K4 methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-02-28T03:15:57Z"
+          "val" : "2010-04-13T11:28:14Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -26418,159 +30578,167 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL9_acceptor_site"
+      "lbl" : "H3K4_methylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000423",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000403",
       "meta" : {
+        "definition" : {
+          "val" : "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates.",
+          "xrefs" : [ "PMID:2551119", "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016" ]
+        },
+        "comments" : [ "An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "R long terminal repeat region",
+          "val" : "snoRNA U14",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "R LTR region",
+          "val" : "small nucleolar RNA U14",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U14 small nucleolar RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U14 snoRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0005839"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "R_LTR_region"
+      "lbl" : "U14_snoRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001793",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001737",
       "meta" : {
         "definition" : {
-          "val" : "A read from an end of the clone sequence.",
+          "val" : "A histone modification, whereby the histone protein is acylated at multiple sites in a region.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "clone end",
+          "pred" : "hasRelatedSynonym",
+          "val" : "histone acylation region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T01:58:21Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-13T11:32:27Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "clone_end"
+      "lbl" : "histone_acylation_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000462",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000072",
       "meta" : {
         "definition" : {
-          "val" : "A non-functional descendant of a functional entity.",
-          "xrefs" : [ "SO:cjm" ]
+          "val" : "A sequence_variant_effect that changes the splice donor sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting splice donor",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "pseudogenic region",
+          "val" : "splice donor mutation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "sequence variant affecting splice donor",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001575"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "pseudogenic_region"
+      "lbl" : "sequence_variant_affecting_splice_donor"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001792",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000406",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes non-coding exon sequence in a non-coding transcript.",
-          "xrefs" : [ "EBI:fc", "SO:ke" ]
+          "val" : "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed.",
+          "xrefs" : [ "PMID:1899376", "PMID:7823908" ]
         },
         "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:non-coding-exon-near-splice",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "Jannovar:non_coding_transcript_exon_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:non_coding_transcript_exon_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:non-coding-exon",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non coding transcript exon variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non_coding_transcript_exon_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "ANNOVAR:ncRNA_exonic",
-          "xrefs" : [ ]
+          "val" : "http://en.wikipedia.org/wiki/Twintron"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-06T01:51:59Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_coding_transcript_exon_variant"
+      "lbl" : "twintron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000461",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000071",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.",
-          "xrefs" : [ "FB:km" ]
+          "val" : "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting splicing",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "inversion derived bipartite deficiency",
+          "val" : "sequence variant affecting splicing",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001568"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "inversion_derived_bipartite_deficiency"
+      "lbl" : "sequence_variant_affecting_splicing"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001311",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000405",
       "meta" : {
         "definition" : {
-          "val" : "N6_N6_dimethyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:080"
+          "val" : "http://en.wikipedia.org/wiki/Y_RNA"
         } ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "m62A",
+          "val" : "INSDC_qualifier:Y_RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6,N6-dimethyladenosine",
+          "val" : "Y RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26579,90 +30747,86 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_N6_dimethyladenosine"
+      "lbl" : "Y_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000464",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000889",
       "meta" : {
         "definition" : {
-          "val" : "A non-functional descendant of an exon.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that is paternally imprinted.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "decayed exon",
+          "val" : "paternally imprinted gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Does not have to be part of a pseudogene."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "decayed_exon"
+      "lbl" : "paternally_imprinted_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001795",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001736",
       "meta" : {
         "definition" : {
-          "val" : "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions.",
-          "xrefs" : [ "PMID:7502067", "SO:vw" ]
+          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "regional centromere",
+          "val" : "H3K9 methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-31T12:43:07Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T11:31:37Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regional_centromere"
+      "lbl" : "H3K9_methylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001794",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000078",
       "meta" : {
         "definition" : {
-          "val" : "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae.",
-          "xrefs" : [ "PMID:7502067", "SO:vw" ]
+          "val" : "A sequence variation that decreases the rate a which transcription of the sequence occurs.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "point centromere",
+          "val" : "sequence variation decreasing rate of transcription",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation decreasing rate of transcription",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-31T12:42:35Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "point_centromere"
+      "lbl" : "sequence_variant_decreasing_rate_of_transcription"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000463",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000884",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes more than one transcript.",
+          "val" : "A stop codon redefined to be the new amino acid, pyrrolysine.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "encodes alternately spliced transcripts",
+          "val" : "stop codon redefined as pyrrolysine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26671,71 +30835,74 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_alternately_spliced_transcripts"
+      "lbl" : "stop_codon_redefined_as_pyrrolysine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001310",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001731",
       "meta" : {
         "definition" : {
-          "val" : "2prime_O_ribosyladenosine_phosphate is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated.",
+          "xrefs" : [ "SO:KE" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:016"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Ar(p)",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "2'-O-ribosyladenosine (phosphate)",
+          "val" : "H4K8ac",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "two prime O ribosyladenosine phosphate",
+          "val" : "H4K8 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "two_prime_O_ribosyladenosine_phosphate"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T11:14:24Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "H4K8_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001791",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000400",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes exon sequence.",
+          "val" : "An attribute describes a quality of sequence.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VAAST:exon_variant",
+          "val" : "sequence attribute",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:exon_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_attribute"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001730",
+      "meta" : {
+        "definition" : {
+          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:EXON",
+          "val" : "H4K5 acetylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:exonic",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "exon variant",
+          "val" : "H4K5ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-06T01:51:17Z"
+          "val" : "2010-04-13T11:13:00Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -26745,76 +30912,93 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exon_variant"
+      "lbl" : "H4K5_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000460",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000883",
       "meta" : {
+        "definition" : {
+          "val" : "A stop codon redefined to be a new amino acid.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vertebrate immunoglobulin T cell receptor segment",
+          "val" : "stop codon read through",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "vertebrate_immunoglobulin/T-cell receptor gene",
+          "pred" : "hasRelatedSynonym",
+          "val" : "stop codon readthrough",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "I am using the term segment instead of gene here to avoid confusion with the region 'gene'."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_segment"
+      "lbl" : "stop_codon_read_through"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001790",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001733",
       "meta" : {
         "definition" : {
-          "val" : "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).",
+          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "paired end fragment",
+          "val" : "H3K36 methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-04-14T01:48:20Z"
+          "val" : "2010-04-13T11:27:28Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "paired_end_fragment"
+      "lbl" : "H3K36_methylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001309",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000076",
       "meta" : {
         "definition" : {
-          "val" : "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Mutation affects the process of transcription, its initiation, progression or termination.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:015"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "two methylthio N6 hydroxynorvalyl carbamoyladenosine",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting transcription",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine",
+          "val" : "sequence variant affecting transcription",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001549"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_variant_affecting_transcription"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000886",
+      "meta" : {
+        "definition" : {
+          "val" : "Recoded mRNA where a block of nucleotides is not translated.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ms2hn6A",
+          "val" : "recoded by translational bypass",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26823,47 +31007,81 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine"
+      "lbl" : "recoded_by_translational_bypass"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000459",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000402",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "enhancer_attribute"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001732",
       "meta" : {
         "definition" : {
-          "val" : "A gene with a transcript that is trans-spliced.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with trans spliced transcript",
+          "val" : "H3K27 methylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-13T11:26:22Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_trans_spliced_transcript"
+      "lbl" : "H3K27_methylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001306",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000075",
       "meta" : {
         "definition" : {
-          "val" : "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Sequence variant affects the editing of the transcript.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:012"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ms2t6A",
+          "val" : "sequence variant affecting editing",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "2-methylthio-N6-threonyl carbamoyladenosine",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting editing",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001544"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_variant_affecting_editing"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000885",
+      "meta" : {
+        "definition" : {
+          "val" : "A stop codon redefined to be the new amino acid, selenocysteine.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two methylthio N6 threonyl carbamoyladenosine",
+          "val" : "stop codon redefined as selenocysteine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26872,25 +31090,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_methylthio_N6_threonyl_carbamoyladenosine"
+      "lbl" : "stop_codon_redefined_as_selenocysteine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000458",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000401",
       "meta" : {
         "definition" : {
-          "val" : "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "An attribute describing a gene.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "D-GENE",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "D gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:D_segment",
+          "val" : "gene attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26899,20 +31109,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "D_gene_segment"
+      "lbl" : "gene_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001789",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001771",
       "meta" : {
         "definition" : {
-          "val" : "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A variant that has been found to be associated with disease.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Mating-type_region"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mating type region",
+          "val" : "disease associated variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26923,32 +31130,29 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-04-08T11:14:07Z"
+          "val" : "2011-03-15T04:05:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mating_type_region"
+      "lbl" : "disease_associated_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001305",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000440",
       "meta" : {
         "definition" : {
-          "val" : "N6_threonylcarbamoyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A replicon that has been modified to act as a vector for foreign sequence.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "xrefs" : [ {
-          "val" : "RNAMOD:011"
+          "val" : "http://en.wikipedia.org/wiki/Vector_(molecular_biology)"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N6 threonylcarbamoyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6-threonylcarbamoyladenosine",
+          "val" : "vector",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "t6A",
+          "val" : "vector replicon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -26957,58 +31161,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_threonylcarbamoyladenosine"
+      "lbl" : "vector_replicon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001308",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001770",
       "meta" : {
         "definition" : {
-          "val" : "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A variant that does not affect the function of the gene or cause disease.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:014"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "hn6A",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6 hydroxynorvalylcarbamoyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6-hydroxynorvalylcarbamoyladenosine",
+          "val" : "benign variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T03:55:40Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_hydroxynorvalylcarbamoyladenosine"
+      "lbl" : "benign_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001307",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000442",
       "meta" : {
         "definition" : {
-          "val" : "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A double stranded oligonucleotide.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:013"
-        } ],
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N6 methyl N6 threonylcarbamoyladenosine",
+          "val" : "ds oligo",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m6t6A",
+          "val" : "ds-oligonucleotide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6-methyl-N6-threonylcarbamoyladenosine",
+          "val" : "double stranded oligonucleotide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27017,77 +31215,85 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_methyl_N6_threonylcarbamoyladenosine"
+      "lbl" : "ds_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000455",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001773",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes an mRNA with a frameshift.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence variant where the mutated gene product does not allow for one or more basic functions necessary for survival.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with mRNA with frameshift",
+          "val" : "lethal variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T04:06:22Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_mRNA_with_frameshift"
+      "lbl" : "lethal_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001786",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001772",
       "meta" : {
         "definition" : {
-          "val" : "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A variant that has been found to cause disease.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "loss of heterozygosity",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "LOH",
+          "val" : "disease causing variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-25T02:32:58Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T04:05:46Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "loss_of_heterozygosity"
+      "lbl" : "disease_causing_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001302",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000441",
       "meta" : {
         "definition" : {
-          "val" : "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A single stranded oligonucleotide.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:008"
-        } ],
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N6 cis hydroxyisopentenyl adenosine",
+          "val" : "single stranded oligonucleotide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "io6A",
+          "val" : "single strand oligonucleotide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6-(cis-hydroxyisopentenyl)adenosine",
+          "val" : "single strand oligo",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ss oligo",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ss oligonucleotide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27096,59 +31302,54 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_cis_hydroxyisopentenyl_adenosine"
+      "lbl" : "ss_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000454",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001768",
       "meta" : {
         "definition" : {
-          "val" : "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.",
-          "xrefs" : [ "http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284" ]
+          "val" : "When a variant has become fixed in the population so that it is now the only variant.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/RasiRNA"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:rasiRNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "repeat associated small interfering RNA",
+          "val" : "fixed variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T03:50:53Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rasiRNA"
+      "lbl" : "fixed_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001301",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000437",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "assortment_derived_duplication"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000436",
       "meta" : {
         "definition" : {
-          "val" : "2_methylthio_N6_isopentenyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:007"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "2-methylthio-N6-isopentenyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "two methylthio N6 isopentenyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ms2i6A",
+          "val" : "autonomously replicating sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27157,14 +31358,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_methylthio_N6_isopentenyladenosine"
+      "lbl" : "ARS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001785",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001767",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
+        "definition" : {
+          "val" : "When a variant from the genomic sequence is commonly found in the general population.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "structural alteration",
+          "val" : "common variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27172,128 +31376,112 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-25T02:27:41Z"
+          "val" : "2011-03-15T03:50:36Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "structural_alteration"
+      "lbl" : "common_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001788",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000439",
       "meta" : {
         "definition" : {
-          "val" : "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription.",
-          "xrefs" : [ "PMID:10556309", "PMID:11577982", "PMID:9649446" ]
+          "val" : "A ring chromosome is a chromosome whose arms have fused together to form a ring in an inverted fashion, often with the loss of the ends of the chromosome.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U-box",
+          "val" : "inverted ring chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-04-08T10:39:14Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U_box"
+      "lbl" : "inverted_ring_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000457",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001769",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome duplication involving an insertion from another chromosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A quality inhering in a variant by virtue of its phenotype.",
+          "xrefs" : [ "PMID:17597783", "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "interchromosomal duplication",
+          "val" : "variant phenotype",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T03:53:15Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "interchromosomal_duplication"
+      "lbl" : "variant_phenotype"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001304",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000438",
       "meta" : {
-        "definition" : {
-          "val" : "N6_glycinylcarbamoyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
-        },
-        "xrefs" : [ {
-          "val" : "RNAMOD:010"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "N6-glycinylcarbamoyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6 glycinylcarbamoyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "g6A",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "N6_glycinylcarbamoyladenosine"
+      "lbl" : "gene_not_polyadenylated"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000456",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001764",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is recombinationally rearranged.",
+          "val" : "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "recombinationally rearranged gene",
+          "val" : "unique variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T03:47:20Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombinationally_rearranged_gene"
+      "lbl" : "unique_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001303",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000433",
       "meta" : {
         "definition" : {
-          "val" : "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:009"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two methylthio N6 cis hydroxyisopentenyl adenosine",
+          "val" : "non LTR retrotransposon polymeric tract",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ms2io6A",
+          "val" : "INSDC_qualifier:non_ltr_retrotransposon_polymeric_tract",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27302,78 +31490,94 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_methylthio_N6_cis_hydroxyisopentenyl_adenosine"
+      "lbl" : "non_LTR_retrotransposon_polymeric_tract"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001787",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000432",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.",
-          "xrefs" : [ "EBI:gr" ]
+          "val" : "The U5 segment of the three-prime long terminal repeat.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice donor 5th base variant",
+          "val" : "U5 three prime LTR region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U5 3' long terminal repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-04-05T04:16:28Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_donor_5th_base_variant"
+      "lbl" : "U5_three_prime_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001782",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001763",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located within a transcription factor binding site.",
-          "xrefs" : [ "EBI:fc" ]
+          "val" : "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population.",
+          "xrefs" : [ "PMID:17597783", "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TF binding site variant",
+          "val" : "variant frequency",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:tf_binding_site_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T03:44:39Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "variant_frequency"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001766",
+      "meta" : {
+        "definition" : {
+          "val" : "A variant that affects one of several possible alleles at that location, such as the major histocompatibility complex (MHC) genes.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:TF_binding_site_variant",
+          "val" : "polymorphic variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-17T10:59:20Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2011-03-15T03:48:51Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TF_binding_site_variant"
+      "lbl" : "polymorphic_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000451",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000435",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a polyadenylated mRNA.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A polypurine tract within an LTR_retrotransposon.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with polyadenylated mRNA",
+          "val" : "RR tract",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "LTR retrotransposon poly purine tract",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27382,17 +31586,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_polyadenylated_mRNA"
+      "lbl" : "RR_tract"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000450",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000434",
       "meta" : {
         "definition" : {
-          "val" : "A light region between two darkly staining bands in a polytene chromosome.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion.",
+          "xrefs" : [ "http://www.koko.gov.my/CocoaBioTech/Glossaryt.html" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "chromosome interband",
+          "pred" : "hasExactSynonym",
+          "val" : "target site duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27401,72 +31605,90 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "interband"
+      "lbl" : "target_site_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001781",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001765",
       "meta" : {
+        "definition" : {
+          "val" : "When a variant from the genomic sequence is rarely found in the general population. The threshold for 'rare' varies between studies.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "de novo variant",
+          "val" : "rare variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:33:34Z"
+          "val" : "2011-03-15T03:48:29Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "de_novo_variant"
+      "lbl" : "rare_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001300",
+      "id" : "http://purl.obolibrary.org/obo/so#BS",
+      "lbl" : "biosapiens"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001760",
       "meta" : {
         "definition" : {
-          "val" : "N6_isopentenyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:006"
-        } ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "non processed pseudogene",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "i6A",
+          "val" : "INSDC_qualifier:unprocessed",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6 isopentenyladenosine",
+          "val" : "unprocessed_pseudogene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6-isopentenyladenosine",
+          "val" : "unprocessed pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-09T10:54:47Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_isopentenyladenosine"
+      "lbl" : "non_processed_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000453",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000431",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.",
-          "xrefs" : [ "FB:reference_manual", "SO:ke" ]
+          "val" : "The U3 segment of the three-prime long terminal repeat.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasNarrowSynonym",
-          "val" : "transposition",
+          "pred" : "hasExactSynonym",
+          "val" : "U3 three prime LTR region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "chromosomal transposition",
+          "val" : "U3 3' long terminal repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27475,111 +31697,91 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_transposition"
+      "lbl" : "U3_three_prime_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001784",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001762",
       "meta" : {
         "definition" : {
-          "val" : "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints.",
-          "xrefs" : [ "FB:reference_manual", "NCBI:th", "SO:ke" ]
+          "val" : "A quality inhering in a variant by virtue of its origin.",
+          "xrefs" : [ "PMID:17597783", "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "complex",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "complex_chromosomal_mutation",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "complex chromosomal mutation",
+          "val" : "variant origin",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000146"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T03:42:13Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-23T03:21:19Z"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "complex_structural_alteration"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000452",
-      "meta" : {
-        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transgene_attribute"
+      "lbl" : "variant_origin"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001780",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000430",
       "meta" : {
+        "definition" : {
+          "val" : "The R segment of the three-prime long terminal repeat.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "population specific variant",
+          "val" : "R three prime LTR region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "R 3' long terminal repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:33:05Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "population_specific_variant"
+      "lbl" : "R_three_prime_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_3000000",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001761",
       "meta" : {
         "definition" : {
-          "val" : "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.",
-          "xrefs" : [ "GOC:add" ]
+          "val" : "A dependent entity that inheres in a bearer, a sequence variant.",
+          "xrefs" : [ "PMID:17597783", "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene segment",
+          "val" : "variant quality",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T03:40:35Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by tracker 2021594, July 2008, by Alex."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_segment"
+      "lbl" : "variant_quality"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001779",
+      "id" : "http://purl.obolibrary.org/obo/so#transcribed_to",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "pedigree specific variant",
-          "xrefs" : [ ]
-        } ],
+        "definition" : {
+          "val" : "Inverse of transcribed_from.",
+          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
+        },
+        "comments" : [ "Example: gene transcribed_to primary_transcript." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:32:18Z"
+          "val" : "2009-08-19T12:08:24Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -27588,18 +31790,22 @@
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "pedigree_specific_variant"
+      "type" : "PROPERTY",
+      "lbl" : "transcribed_to"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000448",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000429",
       "meta" : {
         "definition" : {
-          "val" : "An intron located in the 3' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The U3 segment of the three-prime long terminal repeat.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime UTR intron",
+          "val" : "U3 5' long term repeat region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U3 five prime LTR region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27608,57 +31814,50 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_UTR_intron"
+      "lbl" : "U3_five_prime_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000447",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001757",
       "meta" : {
         "definition" : {
-          "val" : "An intron located in the 5' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime UTR intron",
+          "val" : "SL12 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "five_prime_UTR_intron"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001778",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "germline variant",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:31:46Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2011-02-28T03:17:23Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "germline_variant"
+      "lbl" : "SL12_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000449",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000426",
       "meta" : {
         "definition" : {
-          "val" : "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "The long terminal repeat found at the three-prime end of the sequence to be inserted into the host genome.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "random sequence",
+          "val" : "3' LTR",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "three prime LTR",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3' long terminal repeat",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27667,17 +31866,25 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "random_sequence"
+      "lbl" : "three_prime_LTR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000444",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000425",
       "meta" : {
         "definition" : {
-          "val" : "Non-coding exon in the 3' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The long terminal repeat found at the five-prime end of the sequence to be inserted into the host genome.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime noncoding exon",
+          "val" : "5' LTR",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5' long terminal repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime LTR",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27686,13 +31893,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_noncoding_exon"
+      "lbl" : "five_prime_LTR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001775",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001756",
       "meta" : {
+        "definition" : {
+          "val" : "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "maternal variant",
+          "val" : "SL11 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27700,133 +31911,162 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:30:23Z"
+          "val" : "2011-02-28T03:16:54Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "maternal_variant"
+      "lbl" : "SL11_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000443",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001759",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe the kind of biological sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "SO:ke", "http://en.wikipedia.org/wiki/Pseudogene" ]
         },
+        "comments" : [ "This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polymer attribute",
+          "val" : "INSDC_qualifier:unitary",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "disabled gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "unitary pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-09T10:04:04Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polymer_attribute"
+      "lbl" : "unitary_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001774",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000428",
       "meta" : {
+        "definition" : {
+          "val" : "The U5 segment of the three-prime long terminal repeat.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "quantitative variant",
+          "val" : "U5 5' long terminal repeat region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U5 five prime LTR region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:28:13Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "quantitative_variant"
+      "lbl" : "U5_five_prime_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001777",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000427",
       "meta" : {
+        "definition" : {
+          "val" : "The R segment of the three-prime long terminal repeat.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "somatic variant",
+          "val" : "R 5' long term repeat region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "R five prime LTR region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:31:12Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "somatic_variant"
+      "lbl" : "R_five_prime_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000446",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001758",
       "meta" : {
         "definition" : {
-          "val" : "Intron located in the untranslated region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Pseudogene" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "UTR intron",
+          "pred" : "hasRelatedSynonym",
+          "val" : "duplicated pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-09T09:58:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "UTR_intron"
+      "lbl" : "duplicated_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001776",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001753",
       "meta" : {
+        "definition" : {
+          "val" : "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "paternal variant",
+          "val" : "SL8 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-03-15T04:30:47Z"
+          "val" : "2011-02-28T03:15:26Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "paternal_variant"
+      "lbl" : "SL8_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000445",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000422",
       "meta" : {
         "definition" : {
-          "val" : "Non-coding exon in the 5' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The U5 segment of the long terminal repeats.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5' nc exon",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5' non coding exon",
+          "val" : "U5 LTR region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five prime noncoding exon",
+          "val" : "U5 long terminal repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27835,52 +32075,46 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_noncoding_exon"
+      "lbl" : "U5_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000484",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001752",
       "meta" : {
         "definition" : {
-          "val" : "The sequence of the 3' exon that is not coding.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime coding exon noncoding region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "three_prime_exon_noncoding_region",
+          "val" : "SL37 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T03:13:20Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_coding_exon_noncoding_region"
+      "lbl" : "SL7_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001331",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000421",
       "meta" : {
         "definition" : {
-          "val" : "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "An inverted repeat (SO:0000294) occurring at the 3-prime termini of a DNA transposon.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:036"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two prime O ribosylguanosine phosphate",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Gr(p)",
+          "val" : "three prime terminal inverted repeat",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2'-O-ribosylguanosine (phosphate)",
+          "val" : "3' TIR",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27889,38 +32123,46 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_prime_O_ribosylguanosine_phosphate"
+      "lbl" : "three_prime_terminal_inverted_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000000",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001755",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "definition" : {
+          "val" : "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "SL10 acceptor site",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T03:16:31Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Sequence_Ontology"
+      "lbl" : "SL10_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001330",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000424",
       "meta" : {
         "definition" : {
-          "val" : "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "The U3 segment of the long terminal repeats.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:035"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N2,N2,2'-O-trimethylguanosine",
+          "val" : "U3 LTR region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m22Gmv",
+          "val" : "U3 long terminal repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27929,22 +32171,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N2_N2_2_prime_O_trimethylguanosine"
+      "lbl" : "U3_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000483",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000423",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript that is never translated into a protein.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The R segment of the long terminal repeats.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nc primary transcript",
+          "val" : "R long terminal repeat region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "noncoding primary transcript",
+          "val" : "R LTR region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -27953,67 +32194,68 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nc_primary_transcript"
+      "lbl" : "R_LTR_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001333",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001754",
       "meta" : {
         "definition" : {
-          "val" : "Peroxywybutosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:038"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "o2yW",
+          "val" : "SL9 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-02-28T03:15:57Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "peroxywybutosine"
+      "lbl" : "SL9_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000002",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001793",
       "meta" : {
         "definition" : {
-          "val" : "A folded sequence.",
+          "val" : "A read from an end of the clone sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence secondary structure",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:misc_structure",
+          "val" : "clone end",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-13T11:32:27Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_secondary_structure"
+      "lbl" : "clone_end"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000486",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000462",
       "meta" : {
         "definition" : {
-          "val" : "The sequence of the 5' exon preceding the start codon.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non-functional descendant of a functional entity.",
+          "xrefs" : [ "SO:cjm" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five_prime_exon_noncoding_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five prime coding exon noncoding region",
+          "val" : "pseudogenic region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28022,43 +32264,80 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_coding_exon_noncoding_region"
+      "lbl" : "pseudogenic_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001332",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001792",
       "meta" : {
         "definition" : {
-          "val" : "Wybutosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A sequence variant that changes non-coding exon sequence in a non-coding transcript.",
+          "xrefs" : [ "EBI:fc", "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:037"
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
         } ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "Seattleseq:non-coding-exon-near-splice",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "yW",
+          "val" : "non_coding_transcript_exon_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:non_coding_transcript_exon_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "Jannovar:non_coding_transcript_exon_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:non_coding_exon_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:non-coding-exon",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "ANNOVAR:ncRNA_exonic",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non coding transcript exon variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-06T01:51:59Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "wybutosine"
+      "lbl" : "non_coding_transcript_exon_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000485",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000461",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion.",
+          "xrefs" : [ "FB:km" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "(DJ)-J-CLUSTER",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "DJ J cluster",
+          "val" : "inversion derived bipartite deficiency",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28067,18 +32346,25 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DJ_J_cluster"
+      "lbl" : "inversion_derived_bipartite_deficiency"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000001",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001311",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "N6_N6_dimethyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "RNAMOD:080"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence",
+          "val" : "m62A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N6,N6-dimethyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28087,17 +32373,19 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "region"
+      "lbl" : "N6_N6_dimethyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000480",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000464",
       "meta" : {
         "definition" : {
-          "val" : "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.",
+          "val" : "A non-functional descendant of an exon.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Does not have to be part of a pseudogene." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tiling path clone",
+          "val" : "decayed exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28106,67 +32394,80 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tiling_path_clone"
+      "lbl" : "decayed_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000482",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001795",
       "meta" : {
+        "definition" : {
+          "val" : "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions.",
+          "xrefs" : [ "PMID:7502067", "SO:vw" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vertebrate_immunoglobulin/T-cell receptor gene cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "vertebrate immunoglobulin T cell receptor gene cluster",
+          "val" : "regional centromere",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-31T12:43:07Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_gene_cluster"
+      "lbl" : "regional_centromere"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000481",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001794",
       "meta" : {
         "definition" : {
-          "val" : "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae.",
+          "xrefs" : [ "PMID:7502067", "SO:vw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TIR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "terminal inverted repeat",
+          "val" : "point centromere",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-31T12:42:35Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "terminal_inverted_repeat"
+      "lbl" : "point_centromere"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001328",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001310",
       "meta" : {
         "definition" : {
-          "val" : "N2_N2_dimethylguanosine is a modified guanosine base feature.",
+          "val" : "2prime_O_ribosyladenosine_phosphate is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:033"
+          "val" : "RNAMOD:016"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m22G",
+          "val" : "2'-O-ribosyladenosine (phosphate)",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N2,N2-dimethylguanosine",
+          "val" : "two prime O ribosyladenosine phosphate",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ar(p)",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -28174,28 +32475,41 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N2_N2_dimethylguanosine"
+      "lbl" : "two_prime_O_ribosyladenosine_phosphate"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001327",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000463",
       "meta" : {
         "definition" : {
-          "val" : "2prime_O_methylguanosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A gene that encodes more than one transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:032"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "2'-O-methylguanosine",
+          "val" : "encodes alternately spliced transcripts",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "encodes_alternately_spliced_transcripts"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000460",
+      "meta" : {
+        "definition" : {
+          "val" : "Germline genomic DNA with the sequence for a V, D, C, or J portion of an immunoglobulin/T-cell receptor.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "I am using the term segment instead of gene here to avoid confusion with the region 'gene'." ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Gm",
+          "val" : "vertebrate immunoglobulin T cell receptor segment",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "two prime O methylguanosine",
+          "val" : "vertebrate_immunoglobulin/T-cell receptor gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28204,75 +32518,103 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_prime_O_methylguanosine"
+      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001329",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001791",
       "meta" : {
         "definition" : {
-          "val" : "N2_2prime_O_dimethylguanosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A sequence variant that changes exon sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:034"
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m2Gm",
-          "xrefs" : [ ]
+          "val" : "ANNOVAR:exonic",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N2,2'-O-dimethylguanosine",
+          "val" : "exon variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N2 2 prime O dimethylguanosine",
-          "xrefs" : [ ]
+          "val" : "Jannovar:exon_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:exon_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:EXON",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-06T01:51:17Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N2_2_prime_O_dimethylguanosine"
+      "lbl" : "exon_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000477",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001790",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is polycistronic.",
+          "val" : "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair).",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "paired end fragment",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-04-14T01:48:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polycistronic_gene"
+      "lbl" : "paired_end_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001324",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001309",
       "meta" : {
         "definition" : {
-          "val" : "1_methylguanosine is a modified guanosine base feature.",
+          "val" : "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:029"
+          "val" : "RNAMOD:015"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "one methylguanosine",
+          "val" : "two methylthio N6 hydroxynorvalyl carbamoyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "1-methylguanosine",
-          "xrefs" : [ ]
+          "val" : "ms2hn6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m1G",
+          "val" : "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28281,17 +32623,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "one_methylguanosine"
+      "lbl" : "two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000476",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000459",
       "meta" : {
         "definition" : {
-          "val" : "A DNA sequencer read which is part of a contig.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene with a transcript that is trans-spliced.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "contig read",
+          "val" : "gene with trans spliced transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28300,20 +32642,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "contig_read"
+      "lbl" : "gene_with_trans_spliced_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001323",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001306",
       "meta" : {
         "definition" : {
-          "val" : "Archaeosine is a modified 7-deazoguanosine.",
+          "val" : "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:049"
+          "val" : "RNAMOD:012"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "G+",
+          "val" : "two methylthio N6 threonyl carbamoyladenosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ms2t6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "2-methylthio-N6-threonyl carbamoyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28322,29 +32673,25 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "archaeosine"
+      "lbl" : "two_methylthio_N6_threonyl_carbamoyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000479",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000458",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that is trans-spliced.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "trans spliced transcript",
+          "val" : "D gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "trans-spliced transcript",
+          "val" : "D-GENE",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:trans_splicing",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:tRNA",
+          "val" : "INSDC_feature:D_segment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28353,59 +32700,57 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trans_spliced_transcript"
+      "lbl" : "D_gene_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001326",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001789",
       "meta" : {
         "definition" : {
-          "val" : "7_methylguanosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type.",
+          "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:031"
+          "val" : "http://en.wikipedia.org/wiki/Mating-type_region"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "seven methylguanosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "7-methylguanosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m7G",
+          "val" : "mating type region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-04-08T11:14:07Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "seven_methylguanosine"
+      "lbl" : "mating_type_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000478",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001305",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "N6_threonylcarbamoyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:011"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "C gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "constant gene",
-          "xrefs" : [ ]
+          "val" : "t6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:C_region",
+          "val" : "N6 threonylcarbamoyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "C_GENE",
+          "val" : "N6-threonylcarbamoyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28414,28 +32759,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "C_gene_segment"
+      "lbl" : "N6_threonylcarbamoyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001325",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001308",
       "meta" : {
         "definition" : {
-          "val" : "N2_methylguanosine is a modified guanosine base feature.",
+          "val" : "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:030"
+          "val" : "RNAMOD:014"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N2 methylguanosine",
+          "val" : "N6-hydroxynorvalylcarbamoyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N2-methylguanosine",
-          "xrefs" : [ ]
+          "val" : "hn6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m2G",
+          "val" : "N6 hydroxynorvalylcarbamoyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28444,18 +32790,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N2_methylguanosine"
+      "lbl" : "N6_hydroxynorvalylcarbamoyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000473",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001307",
       "meta" : {
         "definition" : {
-          "val" : "The gene product is involved in its own transcriptional regulation where it decreases transcription.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:013"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "negatively autoregulated",
+          "val" : "N6-methyl-N6-threonylcarbamoyladenosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N6 methyl N6 threonylcarbamoyladenosine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m6t6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -28463,28 +32821,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "negatively_autoregulated"
+      "lbl" : "N6_methyl_N6_threonylcarbamoyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001320",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001302",
       "meta" : {
         "definition" : {
-          "val" : "Mannosyl_queuosine is a modified 7-deazoguanosine.",
+          "val" : "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:046"
+          "val" : "RNAMOD:008"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mannosyl-queuosine",
+          "val" : "N6 cis hydroxyisopentenyl adenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "mannosyl queuosine",
-          "xrefs" : [ ]
+          "val" : "io6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "manQ",
+          "val" : "N6-(cis-hydroxyisopentenyl)adenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28493,48 +32852,47 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mannosyl_queuosine"
+      "lbl" : "N6_cis_hydroxyisopentenyl_adenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000472",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001786",
       "meta" : {
         "definition" : {
-          "val" : "A set of regions which overlap with minimal polymorphism to form a linear sequence.",
-          "xrefs" : [ "SO:cjm" ]
+          "val" : "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tiling path",
+          "val" : "LOH",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "loss of heterozygosity",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-25T02:32:58Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tiling_path"
+      "lbl" : "loss_of_heterozygosity"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001322",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000455",
       "meta" : {
         "definition" : {
-          "val" : "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A gene that encodes an mRNA with a frameshift.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:048"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "preQ1",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "7-aminomethyl-7-deazaguanosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "seven aminomethyl seven deazaguanosine",
+          "val" : "gene with mRNA with frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28543,17 +32901,27 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "seven_aminomethyl_seven_deazaguanosine"
+      "lbl" : "gene_with_mRNA_with_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000475",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000454",
       "meta" : {
         "definition" : {
-          "val" : "The gene product is involved in its own transcriptional regulation, where it increases transcription.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements.",
+          "xrefs" : [ "PMID:18032451", "http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284" ]
         },
+        "comments" : [ "Changed parent term from ncRNA (SO:0000655) to piRNA (SO:0001035). See GitHub Issue #573." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "positively autoregulated",
+          "val" : "repeat associated small interfering RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:rasiRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28562,28 +32930,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "positively_autoregulated"
+      "lbl" : "rasiRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001321",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001301",
       "meta" : {
         "definition" : {
-          "val" : "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.",
+          "val" : "2_methylthio_N6_isopentenyladenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:047"
+          "val" : "RNAMOD:007"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "7-cyano-7-deazaguanosine",
-          "xrefs" : [ ]
+          "val" : "ms2i6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "seven cyano seven deazaguanosine",
+          "val" : "two methylthio N6 isopentenyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "preQ0",
+          "val" : "2-methylthio-N6-isopentenyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28592,70 +32961,99 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "seven_cyano_seven_deazaguanosine"
+      "lbl" : "two_methylthio_N6_isopentenyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000474",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001785",
       "meta" : {
         "definition" : {
-          "val" : "A piece of sequence that makes up a tiling_path (SO:0000472).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An alteration of the genome that leads to a change in the structure of one or more chromosomes.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tiling path fragment",
+          "val" : "structural alteration",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-25T02:27:41Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tiling_path_fragment"
+      "lbl" : "structural_alteration"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#paralogous_to",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001304",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "definition" : {
+          "val" : "N6_glycinylcarbamoyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:010"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "g6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N6-glycinylcarbamoyladenosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N6 glycinylcarbamoyladenosine",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "paralogous_to"
+      "type" : "CLASS",
+      "lbl" : "N6_glycinylcarbamoyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000471",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001788",
       "meta" : {
         "definition" : {
-          "val" : "The gene product is involved in its own transcriptional regulation.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription.",
+          "xrefs" : [ "PMID:10556309", "PMID:11577982", "PMID:9649446" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "U-box",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-04-08T10:39:14Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "autoregulated"
+      "lbl" : "U_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000470",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000457",
       "meta" : {
         "definition" : {
-          "val" : "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A chromosome duplication involving an insertion from another chromosome.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "J-GENE",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "J gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:J_segment",
+          "val" : "interchromosomal duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28664,45 +33062,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "J_gene_segment"
+      "lbl" : "interchromosomal_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001317",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001787",
       "meta" : {
         "definition" : {
-          "val" : "Queuosine is a modified 7-deazoguanosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript.",
+          "xrefs" : [ "EBI:gr" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:043"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Queuosine"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : " Q",
+          "val" : "splice donor 5th base variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-04-05T04:16:28Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "queuosine"
+      "lbl" : "splice_donor_5th_base_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000469",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000456",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a gene sequence where the resulting protein is modified to regulate it.",
+          "val" : "A gene that is recombinationally rearranged.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "post-translationally regulated by protein modification",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "post translationally regulated by protein modification",
+          "val" : "recombinationally rearranged gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28711,21 +33106,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "post_translationally_regulated_by_protein_modification"
+      "lbl" : "recombinationally_rearranged_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001316",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001303",
       "meta" : {
         "definition" : {
-          "val" : "7-deazaguanosine is a modified guanosine.",
+          "val" : "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:009"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "seven deazaguanosine",
+          "val" : "two methylthio N6 cis hydroxyisopentenyl adenosine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "7-deazaguanosine",
+          "pred" : "hasExactSynonym",
+          "val" : "ms2io6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28734,50 +33137,55 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "seven_deazaguanosine"
+      "lbl" : "two_methylthio_N6_cis_hydroxyisopentenyl_adenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001319",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001782",
       "meta" : {
         "definition" : {
-          "val" : "Galactosyl_queuosine is a modified 7-deazoguanosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A sequence variant located within a transcription factor binding site.",
+          "xrefs" : [ "EBI:fc" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:045"
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "galactosyl-queuosine",
-          "xrefs" : [ ]
+          "val" : "VEP:TF_binding_site_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "galQ",
+          "val" : "TF binding site variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "galactosyl queuosine",
-          "xrefs" : [ ]
+          "val" : "Jannovar:tf_binding_site_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-17T10:59:20Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "galactosyl_queuosine"
+      "lbl" : "TF_binding_site_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001318",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000451",
       "meta" : {
         "definition" : {
-          "val" : "Epoxyqueuosine is a modified 7-deazoguanosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A gene that encodes a polyadenylated mRNA.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:044"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "eQ",
+          "val" : "gene with polyadenylated mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28786,92 +33194,103 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "epoxyqueuosine"
+      "lbl" : "gene_with_polyadenylated_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001797",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000450",
       "meta" : {
         "definition" : {
-          "val" : "A repeat region found within the modular centromere.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A light region between two darkly staining bands in a polytene chromosome.",
+          "xrefs" : [ "SO:ma" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:centromeric_repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "centromeric repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "pred" : "hasRelatedSynonym",
+          "val" : "chromosome interband",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-31T12:59:27Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "centromeric_repeat"
+      "lbl" : "interband"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001313",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001781",
       "meta" : {
         "definition" : {
-          "val" : "N6_N6_2prime_O_trimethyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A variant arising in the offspring that is not found in either of the parents.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:089"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m62Am",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6,N6,2'-O-trimethyladenosine",
+          "val" : "de novo variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T04:33:34Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_N6_2_prime_O_trimethyladenosine"
+      "lbl" : "de_novo_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000466",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001784",
       "meta" : {
         "definition" : {
-          "val" : "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints.",
+          "xrefs" : [ "FB:reference_manual", "NCBI:th", "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "variable_gene",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "complex",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbvar"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V gene segment",
+          "val" : "complex_chromosomal_mutation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "V-GENE",
+          "val" : "complex chromosomal mutation",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000146"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-23T03:21:19Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "complex_structural_alteration"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000453",
+      "meta" : {
+        "definition" : {
+          "val" : "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type.",
+          "xrefs" : [ "FB:reference_manual", "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:V_segment",
+          "val" : "chromosomal transposition",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "V gene",
+          "pred" : "hasNarrowSynonym",
+          "val" : "transposition",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28880,28 +33299,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "V_gene_segment"
+      "lbl" : "chromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001312",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001300",
       "meta" : {
         "definition" : {
-          "val" : "N6_2prime_O_dimethyladenosine is a modified adenosine.",
+          "val" : "N6_isopentenyladenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:088"
+          "val" : "RNAMOD:006"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m6Am",
-          "xrefs" : [ ]
+          "val" : "i6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6 2 prime O dimethyladenosine",
+          "val" : "N6 isopentenyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6,2'-O-dimethyladenosine",
+          "val" : "N6-isopentenyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28910,36 +33330,41 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_2_prime_O_dimethyladenosine"
+      "lbl" : "N6_isopentenyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000465",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000452",
       "meta" : {
-        "definition" : {
-          "val" : "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.",
-          "xrefs" : [ "FB:km" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "inversion derived deficiency plus duplication",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "inversion_derived_deficiency_plus_duplication"
+      "lbl" : "transgene_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001796",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001783",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001583"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001780",
       "meta" : {
         "definition" : {
-          "val" : "A conserved region within the central region of a modular centromere, where the kinetochore is formed.",
-          "xrefs" : [ "SO:vw" ]
+          "val" : "A variant found within only speficic populations.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "regional centromere central core",
+          "val" : "population specific variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28950,22 +33375,22 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-31T12:56:30Z"
+          "val" : "2011-03-15T04:33:05Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regional_centromere_central_core"
+      "lbl" : "population_specific_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000468",
+      "id" : "http://purl.obolibrary.org/obo/SO_3000000",
       "meta" : {
         "definition" : {
-          "val" : "One of the pieces of sequence that make up a golden path.",
-          "xrefs" : [ "SO:rd" ]
+          "val" : "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.",
+          "xrefs" : [ "GOC:add" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Requested by tracker 2021594, July 2008, by Alex." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "golden path fragment",
+          "val" : "gene segment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -28974,28 +33399,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "golden_path_fragment"
+      "lbl" : "gene_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001315",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000448",
       "meta" : {
         "definition" : {
-          "val" : "N6_acetyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "An intron located in the 3' UTR.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:102"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ac6A",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6-acetyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6 acetyladenosine",
+          "val" : "three prime UTR intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29004,113 +33418,86 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_acetyladenosine"
+      "lbl" : "three_prime_UTR_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001799",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001779",
       "meta" : {
         "definition" : {
-          "val" : "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms.",
-          "xrefs" : [ "SO:vw" ]
+          "val" : "A variant that is found only by individuals that belong to the same pedigree.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "regional centromere outer repeat region",
+          "val" : "pedigree specific variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-31T01:03:23Z"
+          "val" : "2011-03-15T04:32:18Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regional_centromere_outer_repeat_region"
+      "lbl" : "pedigree_specific_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001314",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001778",
       "meta" : {
         "definition" : {
-          "val" : "1,2'-O-dimethyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A variant present in the embryo that is carried by every cell in the body.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:097"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "one two prime O dimethyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m1Am",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "1,2'-O-dimethyladenosine",
+          "val" : "germline variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T04:31:46Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "one_two_prime_O_dimethyladenosine"
+      "lbl" : "germline_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001798",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000447",
       "meta" : {
         "definition" : {
-          "val" : "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm.",
-          "xrefs" : [ "SO:vw" ]
+          "val" : "An intron located in the 5' UTR.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "regional centromere inner repeat region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "lmr repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "lmr1L",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "lmr1R",
+          "val" : "five prime UTR intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-05-31T01:01:08Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regional_centromere_inner_repeat_region"
+      "lbl" : "five_prime_UTR_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000467",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000449",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components.",
+          "xrefs" : [ "SO:ma" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "post-translationally regulated by protein stability",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "post translationally regulated by protein stability",
+          "val" : "random sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29119,24 +33506,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "post_translationally_regulated_by_protein_stability"
+      "lbl" : "random_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001353",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000444",
       "meta" : {
         "definition" : {
-          "val" : "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Non-coding exon in the 3' UTR.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:061"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3-(3-amino-3-carboxypropyl)uridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "acp3U",
+          "val" : "three prime noncoding exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29145,113 +33525,86 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_three_amino_three_carboxypropyl_uridine"
+      "lbl" : "three_prime_noncoding_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000022",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001775",
       "meta" : {
         "definition" : {
-          "val" : "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A variant in the genetic material inherited from the mother.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "A minor RNA motif",
+          "val" : "maternal variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T04:30:23Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "A_minor_RNA_motif"
+      "lbl" : "maternal_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002201",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001774",
       "meta" : {
         "definition" : {
-          "val" : "A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat.",
+          "val" : "A variant within a gene that contributes to a quantitative trait such as height or weight.",
           "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:terminal",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "terminal repeat",
+          "val" : "quantitative variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T13:00:59Z"
+          "val" : "2011-03-15T04:28:13Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "terminal_repeat"
+      "lbl" : "quantitative_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002202",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000443",
       "meta" : {
         "definition" : {
-          "val" : "A repeat region that is prone to expansions and/or contractions.",
-          "xrefs" : [ ]
+          "val" : "An attribute to describe the kind of biological sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:repeat_instability_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "repeat instability region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_feature",
+          "val" : "polymer attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-09T11:19:55Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "repeat_instability_region"
+      "lbl" : "polymer_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001352",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000446",
       "meta" : {
         "definition" : {
-          "val" : "2_thio_2prime_O_methyluridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Intron located in the untranslated region.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:060"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two thio two prime O methyluridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "2-thio-2'-O-methyluridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "s2Um",
+          "val" : "UTR intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29260,78 +33613,75 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_thio_two_prime_O_methyluridine"
+      "lbl" : "UTR_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000021",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001777",
       "meta" : {
         "definition" : {
-          "val" : "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A variant that has arisen after splitting of the embryo, resulting in the variant being found in only some of the tissues or cells of the body.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "asymmetric RNA internal loop",
+          "val" : "somatic variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T04:31:12Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "asymmetric_RNA_internal_loop"
+      "lbl" : "somatic_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001355",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001776",
       "meta" : {
         "definition" : {
-          "val" : "5_methoxyuridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A variant in the genetic material inherited from the father.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:063"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mo5U",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five methoxyuridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5-methoxyuridine",
+          "val" : "paternal variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-03-15T04:30:47Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_methoxyuridine"
+      "lbl" : "paternal_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000024",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000445",
       "meta" : {
         "definition" : {
-          "val" : "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/7897662" ]
+          "val" : "Non-coding exon in the 5' UTR.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sarcin like RNA motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sarcin/ricin loop",
+          "val" : "five prime noncoding exon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sarcin/ricin domain",
+          "val" : "5' nc exon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sarcin/ricin RNA domain",
+          "val" : "5' non coding exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29340,32 +33690,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sarcin_like_RNA_motif"
+      "lbl" : "five_prime_noncoding_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000023",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000484",
       "meta" : {
         "definition" : {
-          "val" : "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.",
+          "val" : "The sequence of the 3' exon that is not coding.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/K-turn"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "kink-turn motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "K turn RNA motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "kink turn",
+          "val" : "three_prime_exon_noncoding_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "K-turn",
+          "val" : "three prime coding exon noncoding region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29374,61 +33714,68 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "K_turn_RNA_motif"
+      "lbl" : "three_prime_coding_exon_noncoding_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002200",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001331",
       "meta" : {
         "definition" : {
-          "val" : "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.",
-          "xrefs" : [ ]
+          "val" : "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:036"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "allelic pseudogenic tRNA",
+          "val" : "2'-O-ribosylguanosine (phosphate)",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:allelic",
+          "val" : "two prime O ribosylguanosine phosphate",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:tRNA",
-          "xrefs" : [ ]
+          "val" : "Gr(p)",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T12:18:38Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "allelic_pseudogenic_tRNA"
+      "lbl" : "two_prime_O_ribosylguanosine_phosphate"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001354",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000000",
+      "meta" : {
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "Sequence_Ontology"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001330",
       "meta" : {
         "definition" : {
-          "val" : "5_hydroxyuridine is a modified uridine base feature.",
+          "val" : "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:060"
+          "val" : "RNAMOD:035"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ho5U",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five hydroxyuridine",
-          "xrefs" : [ ]
+          "val" : "m22Gmv",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-hydroxyuridine",
+          "val" : "N2,N2,2'-O-trimethylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29437,17 +33784,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_hydroxyuridine"
+      "lbl" : "N2_N2_2_prime_O_trimethylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000020",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000483",
       "meta" : {
         "definition" : {
-          "val" : "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.",
+          "val" : "A primary transcript that is never translated into a protein.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA internal loop",
+          "val" : "noncoding primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "nc primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29456,28 +33808,45 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_internal_loop"
+      "lbl" : "nc_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001351",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001333",
       "meta" : {
         "definition" : {
-          "val" : "5_methyl_2_thiouridine is a modified uridine base feature.",
+          "val" : "Peroxywybutosine is a modified guanosine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:059"
+          "val" : "RNAMOD:038"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5-methyl-2-thiouridine",
-          "xrefs" : [ ]
-        }, {
+          "val" : "o2yW",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "peroxywybutosine"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000486",
+      "meta" : {
+        "definition" : {
+          "val" : "The sequence of the 5' exon preceding the start codon.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m5s2U",
+          "val" : "five_prime_exon_noncoding_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five methyl 2 thiouridine",
+          "val" : "five prime coding exon noncoding region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29486,28 +33855,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_methyl_2_thiouridine"
+      "lbl" : "five_prime_coding_exon_noncoding_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001350",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000002",
       "meta" : {
         "definition" : {
-          "val" : "4_thiouridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A folded sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:058"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "s4U",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "4-thiouridine",
+          "val" : "sequence secondary structure",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "four thiouridine",
+          "val" : "INSDC_feature:misc_structure",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29516,28 +33878,41 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "four_thiouridine"
+      "lbl" : "sequence_secondary_structure"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001349",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000001",
       "meta" : {
         "definition" : {
-          "val" : "2_thiouridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:057"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "s2U",
+          "val" : "sequence",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "region"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000485",
+      "meta" : {
+        "definition" : {
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two thiouridine",
+          "val" : "DJ J cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2-thiouridine",
+          "val" : "(DJ)-J-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29546,21 +33921,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_thiouridine"
+      "lbl" : "DJ_J_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000018",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001332",
       "meta" : {
         "definition" : {
-          "val" : "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.",
-          "xrefs" : [ "ISBN:038752046" ]
+          "val" : "Wybutosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Linkage_group"
+          "val" : "RNAMOD:037"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "linkage group",
-          "xrefs" : [ ]
+          "val" : "yW",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -29568,18 +33944,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "linkage_group"
+      "lbl" : "wybutosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000499",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000480",
       "meta" : {
         "definition" : {
-          "val" : "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.",
+          "val" : "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "virtual sequence",
+          "val" : "tiling path clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29588,28 +33963,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "virtual_sequence"
+      "lbl" : "tiling_path_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001346",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000482",
       "meta" : {
         "definition" : {
-          "val" : "5_2_prime_O_dimethyluridine is a modified uridine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:054"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m5Um",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5,2'-O-dimethyluridine",
+          "val" : "vertebrate_immunoglobulin/T-cell receptor gene cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five two prime O dimethyluridine",
+          "val" : "vertebrate immunoglobulin T cell receptor gene cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29618,58 +33986,48 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_two_prime_O_dimethyluridine"
+      "lbl" : "vertebrate_immunoglobulin_T_cell_receptor_gene_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000015",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000481",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).",
-          "xrefs" : [ "PMID:12651739:12537576", "PMID:16858867" ]
+          "val" : "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DPE motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "CRWMGCGWKCGCTTS",
+          "val" : "terminal inverted repeat",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "downstream core promoter element",
+          "val" : "TIR",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Binds TAF6, TAF9."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DPE_motif"
+      "lbl" : "terminal_inverted_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001345",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001328",
       "meta" : {
         "definition" : {
-          "val" : "2prime_O_methyluridine is a modified uridine base feature.",
+          "val" : "N2_N2_dimethylguanosine is a modified guanosine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:053"
+          "val" : "RNAMOD:033"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two prime O methyluridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "2'-O-methyluridine",
-          "xrefs" : [ ]
+          "val" : "m22G",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Um",
+          "val" : "N2,N2-dimethylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29678,26 +34036,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_prime_O_methyluridine"
+      "lbl" : "N2_N2_dimethylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000498",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001327",
       "meta" : {
         "definition" : {
-          "val" : "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "2prime_O_methylguanosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:032"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime D spacer",
+          "val" : "2'-O-methylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five prime D-spacer",
+          "val" : "two prime O methylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5'-SPACER",
-          "xrefs" : [ ]
+          "val" : "Gm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -29705,62 +34067,60 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_D_spacer"
+      "lbl" : "two_prime_O_methylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000014",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001329",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.",
-          "xrefs" : [ "PMID:12651739", "PMID:16858867" ]
+          "val" : "N2_2prime_O_dimethylguanosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:034"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "DMp2",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "INR motif",
+          "val" : "N2 2 prime O dimethylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "initiator",
+          "val" : "N2,2'-O-dimethylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "initiator motif",
-          "xrefs" : [ ]
+          "val" : "m2Gm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Binds TAF1, TAF2."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "INR_motif"
+      "lbl" : "N2_2_prime_O_dimethylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001348",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001324",
       "meta" : {
         "definition" : {
-          "val" : "2prime_O_methylpseudouridine is a modified uridine base feature.",
+          "val" : "1_methylguanosine is a modified guanosine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:056"
+          "val" : "RNAMOD:029"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two prime O methylpseudouridine",
+          "val" : "1-methylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2'-O-methylpseudouridine",
-          "xrefs" : [ ]
+          "val" : "m1G",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Ym",
+          "val" : "one methylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29769,94 +34129,56 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_prime_O_methylpseudouridine"
+      "lbl" : "one_methylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000017",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000477",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G).",
-          "xrefs" : [ "PMID:12651739" ]
+          "val" : "A gene that is polycistronic.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "PSE motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "proximal sequence element",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "PSE_motif"
+      "lbl" : "polycistronic_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000016",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000476",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.",
-          "xrefs" : [ "PMID:12651739", "PMID:16858867" ]
+          "val" : "A DNA sequencer read which is part of a contig.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "BRE motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "B-recognition element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "transcription factor B-recognition element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "TFIIB recognition element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "BREu motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "BREu",
+          "val" : "contig read",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Binds TFIIB."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "BREu_motif"
+      "lbl" : "contig_read"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001347",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001323",
       "meta" : {
         "definition" : {
-          "val" : "1_methylpseudouridine is a modified uridine base feature.",
+          "val" : "Archaeosine is a modified 7-deazoguanosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:055"
+          "val" : "RNAMOD:049"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "one methylpseudouridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "1-methylpseudouridine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m1Y",
-          "xrefs" : [ ]
+          "val" : "G+",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -29864,20 +34186,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "one_methylpseudouridine"
+      "lbl" : "archaeosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001342",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001326",
       "meta" : {
         "definition" : {
-          "val" : "Isowyosine is a modified guanosine base feature.",
+          "val" : "7_methylguanosine is a modified guanosine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:101"
+          "val" : "RNAMOD:031"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "imG2",
+          "val" : "7-methylguanosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m7G",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "seven methylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29886,13 +34217,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "isowyosine"
+      "lbl" : "seven_methylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000011",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000479",
       "meta" : {
+        "definition" : {
+          "val" : "A transcript that is trans-spliced.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non protein-coding",
+          "val" : "INSDC_qualifier:trans_splicing",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "trans spliced transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "trans-spliced transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29901,21 +34248,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_protein_coding"
+      "lbl" : "trans_spliced_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000495",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000478",
       "meta" : {
         "definition" : {
-          "val" : "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.",
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205).",
           "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime D spacer",
+          "val" : "C_GENE",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "3'D-SPACER",
+          "val" : "INSDC_feature:C_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "constant gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "C gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29924,28 +34279,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_D_spacer"
+      "lbl" : "C_gene_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001341",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001325",
       "meta" : {
         "definition" : {
-          "val" : "4_demethylwyosine is a modified guanosine base feature.",
+          "val" : "N2_methylguanosine is a modified guanosine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:100"
+          "val" : "RNAMOD:030"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "4-demethylwyosine",
-          "xrefs" : [ ]
+          "val" : "m2G",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "imG-14",
+          "val" : "N2-methylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "four demethylwyosine",
+          "val" : "N2 methylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29954,36 +34310,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "four_demethylwyosine"
+      "lbl" : "N2_methylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000494",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000473",
       "meta" : {
         "definition" : {
-          "val" : "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "The gene product is involved in its own transcriptional regulation where it decreases transcription.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime D nonamer",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "3'D-NOMAMER",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "three_prime_D_nonamer"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000010",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "protein-coding",
+          "val" : "negatively autoregulated",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -29992,26 +34329,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "protein_coding"
+      "lbl" : "negatively_autoregulated"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000013",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001320",
       "meta" : {
         "definition" : {
-          "val" : "A small non coding RNA sequence, present in the cytoplasm.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Mannosyl_queuosine is a modified 7-deazoguanosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "RNAMOD:046"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "small cytoplasmic RNA",
-          "xrefs" : [ ]
+          "val" : "manQ",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:scRNA",
+          "val" : "mannosyl-queuosine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "mannosyl queuosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30020,21 +34360,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "scRNA"
+      "lbl" : "mannosyl_queuosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000497",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000472",
       "meta" : {
         "definition" : {
-          "val" : "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A set of regions which overlap with minimal polymorphism to form a linear sequence.",
+          "xrefs" : [ "SO:cjm" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime D nonamer",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5'D-NONAMER",
+          "val" : "tiling path",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30043,30 +34380,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_D_nonamer"
+      "lbl" : "tiling_path"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001344",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001322",
       "meta" : {
         "definition" : {
-          "val" : "5_methyluridine is a modified uridine base feature.",
+          "val" : "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/5-methyluridine"
-        }, {
-          "val" : "RNAMOD:052"
+          "val" : "RNAMOD:048"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5-methyluridine",
+          "val" : "seven aminomethyl seven deazaguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m5U",
-          "xrefs" : [ ]
+          "val" : "preQ1",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five methyluridine",
+          "val" : "7-aminomethyl-7-deazaguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30075,33 +34411,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_methyluridine"
+      "lbl" : "seven_aminomethyl_seven_deazaguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000012",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000475",
       "meta" : {
         "definition" : {
-          "val" : "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html" ]
+          "val" : "The gene product is involved in its own transcriptional regulation, where it increases transcription.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "scRNA primary transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small cytoplasmic RNA transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "small cytoplasmic RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "small_cytoplasmic_RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "scRNA transcript",
+          "val" : "positively autoregulated",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30110,29 +34430,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "scRNA_primary_transcript"
+      "lbl" : "positively_autoregulated"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001343",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001321",
       "meta" : {
         "definition" : {
-          "val" : "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.",
+          "val" : "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:106"
+          "val" : "RNAMOD:047"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m2,7Gm",
+          "val" : "7-cyano-7-deazaguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N2 7 2prirme O trimethylguanosine",
+          "val" : "seven cyano seven deazaguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N2,7,2'-O-trimethylguanosine",
-          "xrefs" : [ ]
+          "val" : "preQ0",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30140,21 +34461,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N2_7_2prirme_O_trimethylguanosine"
+      "lbl" : "seven_cyano_seven_deazaguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000496",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000474",
       "meta" : {
         "definition" : {
-          "val" : "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A piece of sequence that makes up a tiling_path (SO:0000472).",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime D heptamer",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5'D-HEPTAMER",
+          "val" : "tiling path fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30163,67 +34481,50 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_D_heptamer"
+      "lbl" : "tiling_path_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000491",
+      "id" : "http://purl.obolibrary.org/obo/so#paralogous_to",
       "meta" : {
-        "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "(VJ)-J-CLUSTER",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VJ J cluster",
-          "xrefs" : [ ]
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "VJ_J_cluster"
+      "type" : "PROPERTY",
+      "lbl" : "paralogous_to"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000490",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000471",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "The gene product is involved in its own transcriptional regulation.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "(VJ)-J-C-CLUSTER",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VJ J C cluster",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "VJ_J_C_cluster"
+      "lbl" : "autoregulated"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000493",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000470",
       "meta" : {
         "definition" : {
-          "val" : "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.",
+          "val" : "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment.",
           "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3'D-HEPTAMER",
+          "val" : "INSDC_feature:J_segment",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "three prime D heptamer",
+          "val" : "J-GENE",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "J gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30232,29 +34533,24 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_D_heptamer"
+      "lbl" : "J_gene_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001340",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001317",
       "meta" : {
         "definition" : {
-          "val" : "1_2prime_O_dimethylguanosine is a modified guanosine base feature.",
+          "val" : "Queuosine is a modified 7-deazoguanosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:096"
+          "val" : "http://en.wikipedia.org/wiki/Queuosine"
+        }, {
+          "val" : "RNAMOD:043"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "1,2'-O-dimethylguanosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m1Gm",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "one two prime O dimethylguanosine",
-          "xrefs" : [ ]
+          "val" : " Q",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30262,13 +34558,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "one_two_prime_O_dimethylguanosine"
+      "lbl" : "queuosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000492",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000469",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute describing a gene sequence where the resulting protein is modified to regulate it.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "D gene recombination feature",
+          "val" : "post translationally regulated by protein modification",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "post-translationally regulated by protein modification",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30277,37 +34581,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "D_gene_recombination_feature"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000008",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "gene_sensu_your_favorite_organism"
+      "lbl" : "post_translationally_regulated_by_protein_modification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001339",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001316",
       "meta" : {
         "definition" : {
-          "val" : "N2_N2_7_trimethylguanosine is a modified guanosine base feature.",
+          "val" : "7-deazaguanosine is a modified guanosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:091"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m2,2,7G",
+          "val" : "seven deazaguanosine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N2,N2,7-trimethylguanosine",
+          "pred" : "hasRelatedSynonym",
+          "val" : "7-deazaguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30316,28 +34604,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N2_N2_7_trimethylguanosine"
+      "lbl" : "seven_deazaguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001338",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001319",
       "meta" : {
         "definition" : {
-          "val" : "N2_7_dimethylguanosine is a modified guanosine base feature.",
+          "val" : "Galactosyl_queuosine is a modified 7-deazoguanosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:090"
+          "val" : "RNAMOD:045"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N2,7-dimethylguanosine",
-          "xrefs" : [ ]
+          "val" : "galQ",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m2,7G",
+          "val" : "galactosyl-queuosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N2 7 dimethylguanosine",
+          "val" : "galactosyl queuosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30346,23 +34635,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N2_7_dimethylguanosine"
+      "lbl" : "galactosyl_queuosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000007",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001318",
       "meta" : {
         "definition" : {
-          "val" : "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.",
-          "xrefs" : [ "SO:ls" ]
+          "val" : "Epoxyqueuosine is a modified 7-deazoguanosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "RNAMOD:044"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mate pair",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "read-pair",
-          "xrefs" : [ ]
+          "val" : "eQ",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30370,50 +34658,66 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "read_pair"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000009",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "gene_class"
+      "lbl" : "epoxyqueuosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000004",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001797",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "definition" : {
+          "val" : "A repeat region found within the modular centromere.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "interior coding exon",
+          "val" : "centromeric repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:centromeric_repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-31T12:59:27Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "interior_coding_exon"
+      "lbl" : "centromeric_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000488",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000466",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.",
+          "val" : "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR.",
           "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "(VDJ)-J-CLUSTER",
+          "val" : "V gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VDJ J cluster",
+          "val" : "V-GENE",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "variable_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "V gene segment",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:V_segment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30422,25 +34726,26 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "VDJ_J_cluster"
+      "lbl" : "V_gene_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001335",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001313",
       "meta" : {
         "definition" : {
-          "val" : "Undermodified_hydroxywybutosine is a modified guanosine base feature.",
+          "val" : "N6_N6_2prime_O_trimethyladenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:040"
+          "val" : "RNAMOD:089"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "undermodified hydroxywybutosine",
+          "val" : "N6,N6,2'-O-trimethyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "OHyW*",
-          "xrefs" : [ ]
+          "val" : "m62Am",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30448,71 +34753,54 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "undermodified_hydroxywybutosine"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty",
-      "type" : "PROPERTY",
-      "lbl" : "subset_property"
+      "lbl" : "N6_N6_2_prime_O_trimethyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000487",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001796",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A conserved region within the central region of a modular centromere, where the kinetochore is formed.",
+          "xrefs" : [ "SO:vw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VDJ J C cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "(VDJ)-J-C-CLUSTER",
+          "val" : "regional centromere central core",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-31T12:56:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "VDJ_J_C_cluster"
+      "lbl" : "regional_centromere_central_core"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000003",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001312",
       "meta" : {
         "definition" : {
-          "val" : "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract" ]
+          "val" : "N6_2prime_O_dimethyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/G-quadruplex"
+          "val" : "RNAMOD:088"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "G_quadruplex",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "G-quartet",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "G tetrad",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "guanine tetrad",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "G-tetrad",
-          "xrefs" : [ ]
+          "val" : "m6Am",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "G quartet",
+          "val" : "N6,2'-O-dimethyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "G-quadruplex",
+          "val" : "N6 2 prime O dimethyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30521,20 +34809,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "G_quartet"
+      "lbl" : "N6_2_prime_O_dimethyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001334",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000465",
       "meta" : {
         "definition" : {
-          "val" : "Hydroxywybutosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion.",
+          "xrefs" : [ "FB:km" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:039"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "OHyW",
+          "val" : "inversion derived deficiency plus duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30543,72 +34828,74 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "hydroxywybutosine"
+      "lbl" : "inversion_derived_deficiency_plus_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000006",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000468",
       "meta" : {
         "definition" : {
-          "val" : "A region amplified by a PCR reaction.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "One of the pieces of sequence that make up a golden path.",
+          "xrefs" : [ "SO:rd" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/RAPD"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "amplicon",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "PCR product",
+          "val" : "golden path fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "PCR_product"
+      "lbl" : "golden_path_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001337",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001799",
       "meta" : {
         "definition" : {
-          "val" : "Methylwyosine is a modified guanosine base feature.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms.",
+          "xrefs" : [ "SO:vw" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:042"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mimG",
+          "val" : "regional centromere outer repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2011-05-31T01:03:23Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "methylwyosine"
+      "lbl" : "regional_centromere_outer_repeat_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001336",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001315",
       "meta" : {
         "definition" : {
-          "val" : "Wyosine is a modified guanosine base feature.",
+          "val" : "N6_acetyladenosine is a modified adenosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:041"
+          "val" : "RNAMOD:102"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "IMG",
+          "val" : "N6 acetyladenosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ac6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N6-acetyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30617,22 +34904,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "wyosine"
+      "lbl" : "N6_acetyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000489",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001314",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "1,2'-O-dimethyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:097"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(VJ)-C-CLUSTER",
+          "pred" : "hasExactSynonym",
+          "val" : "1,2'-O-dimethyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VJ C cluster",
+          "val" : "one two prime O dimethyladenosine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m1Am",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30640,29 +34935,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "VJ_C_cluster"
+      "lbl" : "one_two_prime_O_dimethyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000005",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000467",
       "meta" : {
         "definition" : {
-          "val" : "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Satellite_DNA"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "pred" : "hasExactSynonym",
+          "val" : "post translationally regulated by protein stability",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:satellite",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "satellite DNA",
+          "val" : "post-translationally regulated by protein stability",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30671,122 +34958,95 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "satellite_DNA"
+      "lbl" : "post_translationally_regulated_by_protein_stability"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002102",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001798",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of  an immunoglobulin chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm.",
+          "xrefs" : [ "SO:vw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin variable pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "IG_variable_pseudogene",
+          "val" : "lmr1L",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin_variable_pseudogene",
+          "val" : "lmr1R",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IG variable pseudogene",
+          "val" : "lmr repeat",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IG V pseudogene",
+          "val" : "regional centromere inner repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:05:56Z"
+          "val" : "2011-05-31T01:01:08Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "IG_V_pseudogene"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001254",
-      "meta" : {
-        "definition" : {
-          "val" : "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Polyploid"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polyploid"
+      "lbl" : "regional_centromere_inner_repeat_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002103",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002201",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of  an immunoglobulin chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T cell receptor Variable pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_V_pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "TR V pseudogene",
+          "val" : "INSDC_qualifier:terminal",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "T cell receptor V pseudogene",
+          "val" : "terminal repeat",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_Variable_pseudogene",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:06:29Z"
+          "val" : "2018-01-08T13:00:59Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TR_V_pseudogene"
+      "lbl" : "terminal_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001253",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001353",
       "meta" : {
         "definition" : {
-          "val" : "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:061"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sonicate fragment",
+          "val" : "acp3U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3-(3-amino-3-carboxypropyl)uridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30795,16 +35055,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sonicate_fragment"
+      "lbl" : "three_three_amino_three_carboxypropyl_uridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001256",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000022",
       "meta" : {
         "definition" : {
-          "val" : "A polyploid where the multiple chromosome set was derived from a different organism.",
+          "val" : "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Allopolyploid"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "A minor RNA motif",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30812,88 +35074,82 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "allopolyploid"
+      "lbl" : "A_minor_RNA_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002100",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002202",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "A repeat region that is prone to expansions and/or contractions.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "IG C pseudogene",
+          "val" : "repeat instability region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_note:repeat_instability_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
+          "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:05:08Z"
+          "val" : "2018-01-09T11:19:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "IG_C_pseudogene"
+      "lbl" : "repeat_instability_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002101",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001352",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "2_thio_2prime_O_methyluridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:060"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "IG joining pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "IG_joining_pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin_Joining_Pseudogene",
+          "val" : "two thio two prime O methyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IG J pseudogene",
+          "val" : "2-thio-2'-O-methyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin Joining Pseudogene",
-          "xrefs" : [ ]
+          "val" : "s2Um",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:05:34Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "IG_J_pseudogene"
+      "lbl" : "two_thio_two_prime_O_methyluridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001255",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000021",
       "meta" : {
         "definition" : {
-          "val" : "A polyploid where the multiple chromosome set was derived from the same organism.",
+          "val" : "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Autopolyploid"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "asymmetric RNA internal loop",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30901,34 +35157,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "autopolyploid"
+      "lbl" : "asymmetric_RNA_internal_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001250",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001355",
       "meta" : {
         "definition" : {
-          "val" : "A fingerprint_map is a physical map composed of restriction fragments.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "5_methoxyuridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:063"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "BACmap",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "FPCmap",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "FPC",
+          "val" : "5-methoxyuridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "restriction map",
+          "val" : "five methoxyuridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "fingerprint map",
-          "xrefs" : [ ]
+          "val" : "mo5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -30936,21 +35188,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "fingerprint_map"
+      "lbl" : "five_methoxyuridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001252",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000024",
       "meta" : {
         "definition" : {
-          "val" : "A radiation hybrid map is a physical map.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/7897662" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RH map",
+          "val" : "sarcin/ricin loop",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "radiation hybrid map",
+          "val" : "sarcin like RNA motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sarcin/ricin domain",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sarcin/ricin RNA domain",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30959,17 +35219,32 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RH_map"
+      "lbl" : "sarcin_like_RNA_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001251",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000023",
       "meta" : {
         "definition" : {
-          "val" : "An STS map is a physical map organized by the unique STS landmarks.",
+          "val" : "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/K-turn"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "STS map",
+          "val" : "K-turn",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "K turn RNA motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "kink-turn motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "kink turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -30978,53 +35253,63 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "STS_map"
+      "lbl" : "K_turn_RNA_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001247",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002200",
       "meta" : {
         "definition" : {
-          "val" : "An oligo composed of synthetic nucleotides.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "synthetic oligo",
+          "val" : "allelic pseudogenic tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:allelic",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:tRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T12:18:38Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "synthetic_oligo"
+      "lbl" : "allelic_pseudogenic_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000399",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001354",
       "meta" : {
         "definition" : {
-          "val" : "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007" ]
+          "val" : "5_hydroxyuridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/U12_snRNA"
+          "val" : "RNAMOD:060"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U12 small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "ho5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U12 snRNA",
+          "val" : "5-hydroxyuridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA U12",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U12",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "five hydroxyuridine",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31032,17 +35317,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U12_snRNA"
+      "lbl" : "five_hydroxyuridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001246",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000020",
       "meta" : {
         "definition" : {
-          "val" : "The loop of the hairpin loop formed by folding of the pre-miRNA.",
+          "val" : "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miRNA loop",
+          "val" : "RNA internal loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31051,22 +35336,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miRNA_loop"
+      "lbl" : "RNA_internal_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001249",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001351",
       "meta" : {
         "definition" : {
-          "val" : "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "5_methyl_2_thiouridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:059"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "physical map",
+          "val" : "five methyl 2 thiouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "fragment assembly",
+          "val" : "5-methyl-2-thiouridine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m5s2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31074,36 +35367,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "fragment_assembly"
+      "lbl" : "five_methyl_2_thiouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001248",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001350",
       "meta" : {
         "definition" : {
-          "val" : "A region of the genome of known length that is composed by ordering and aligning two or more different regions.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "4_thiouridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly"
+          "val" : "RNAMOD:058"
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "assembly"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001243",
-      "meta" : {
-        "definition" : {
-          "val" : "A part of an miRNA primary_transcript.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miRNA primary transcript region",
+          "val" : "4-thiouridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "four thiouridine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "s4U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31111,34 +35398,43 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miRNA_primary_transcript_region"
+      "lbl" : "four_thiouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000396",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000019",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000313"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001349",
       "meta" : {
         "definition" : {
-          "val" : "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015" ]
+          "val" : "2_thiouridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/U6_snRNA"
+          "val" : "RNAMOD:057"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U6 snRNA",
+          "val" : "two thiouridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U6 small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snRNA U6",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "s2U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U6",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "2-thiouridine",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31146,33 +35442,20 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U6_snRNA"
+      "lbl" : "two_thiouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000395",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000018",
       "meta" : {
         "definition" : {
-          "val" : "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020" ]
+          "val" : "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned.",
+          "xrefs" : [ "ISBN:038752046" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/U5_snRNA"
+          "val" : "http://en.wikipedia.org/wiki/Linkage_group"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U5 small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U5",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snRNA U5",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U5 snRNA",
+          "val" : "linkage group",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31181,34 +35464,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U5_snRNA"
+      "lbl" : "linkage_group"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000398",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001346",
       "meta" : {
         "definition" : {
-          "val" : "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.",
-          "xrefs" : [ "PMID:9622129" ]
+          "val" : "5_2_prime_O_dimethyluridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/U11_snRNA"
+          "val" : "RNAMOD:054"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA U11",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "m5Um",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U11 snRNA",
+          "val" : "five two prime O dimethyluridine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U11",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U11 small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "5,2'-O-dimethyluridine",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31216,17 +35495,26 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U11_snRNA"
+      "lbl" : "five_two_prime_O_dimethyluridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001245",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000015",
       "meta" : {
         "definition" : {
-          "val" : "The stem of the hairpin loop formed by folding of the pre-miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C).",
+          "xrefs" : [ "PMID:12515390", "PMID:12537576", "PMID:12651739", "PMID:16858867" ]
         },
+        "comments" : [ "Binds TAF6, TAF9." ],
         "synonyms" : [ {
+          "pred" : "hasNarrowSynonym",
+          "val" : "CRWMGCGWKCGCTTS",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "miRNA stem",
+          "val" : "downstream core promoter element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DPE motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31235,27 +35523,19 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miRNA_stem"
+      "lbl" : "DPE_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000397",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000499",
       "meta" : {
         "definition" : {
-          "val" : "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract" ]
+          "val" : "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database.",
+          "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA U6atac",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U6atac snRNA",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U6atac small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "virtual sequence",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31263,18 +35543,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U6atac_snRNA"
+      "lbl" : "virtual_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001244",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001345",
       "meta" : {
         "definition" : {
-          "val" : "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "2prime_O_methyluridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:053"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pre-miRNA",
+          "val" : "two prime O methyluridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "2'-O-methyluridine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Um",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31282,33 +35574,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pre_miRNA"
+      "lbl" : "two_prime_O_methyluridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000392",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000014",
       "meta" : {
         "definition" : {
-          "val" : "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element.",
+          "xrefs" : [ "PMID:12651739", "PMID:16858867" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/U2_snRNA"
-        } ],
+        "comments" : [ "Binds TAF1, TAF2." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U2",
-          "xrefs" : [ "RSC:CB" ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "DMp2",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA U2",
-          "xrefs" : [ "RSC:CB" ]
+          "val" : "INR motif",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U2 small nuclear RNA",
-          "xrefs" : [ "RSC:CB" ]
+          "val" : "initiator",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U2 snRNA",
+          "val" : "initiator motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31317,34 +35606,26 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U2_snRNA"
+      "lbl" : "INR_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000391",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000498",
       "meta" : {
         "definition" : {
-          "val" : "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003" ]
+          "val" : "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/U1_snRNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U1 snRNA",
+          "val" : "five prime D spacer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U1",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snRNA U1",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "5'-SPACER",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U1 small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "five prime D-spacer",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31352,45 +35633,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U1_snRNA"
+      "lbl" : "five_prime_D_spacer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000394",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000017",
       "meta" : {
         "definition" : {
-          "val" : "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).",
-          "xrefs" : [ "PMID:=12409455" ]
+          "val" : "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes.",
+          "xrefs" : [ "PMID:11390411", "PMID:12621023", "PMID:12651739", "PMID:23166507", "PMID:8339931" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U4atac snRNA",
+          "val" : "PSE motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA U4atac",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U4atac",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U4atac small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "U4atac_snRNA"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001241",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "encodes alternate transcription start sites",
+          "val" : "proximal sequence element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31399,17 +35656,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_alternate_transcription_start_sites"
+      "lbl" : "PSE_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001240",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001348",
       "meta" : {
         "definition" : {
-          "val" : "The region of a gene from the 5' most TSS to the 3' TSS.",
-          "xrefs" : [ "BBOP:nw" ]
+          "val" : "2prime_O_methylpseudouridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:056"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TSS region",
+          "val" : "2'-O-methylpseudouridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ym",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "two prime O methylpseudouridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31418,33 +35687,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TSS_region"
+      "lbl" : "two_prime_O_methylpseudouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000393",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001347",
       "meta" : {
         "definition" : {
-          "val" : "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015" ]
+          "val" : "1_methylpseudouridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/U4_snRNA"
+          "val" : "RNAMOD:055"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA U4",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA U4",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "m1Y",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U4 small nuclear RNA",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "one methylpseudouridine",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "U4 snRNA",
+          "val" : "1-methylpseudouridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31453,29 +35718,38 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U4_snRNA"
+      "lbl" : "one_methylpseudouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000390",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000016",
       "meta" : {
         "definition" : {
-          "val" : "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB.",
+          "xrefs" : [ "PMID:12651739", "PMID:16858867" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Telomerase_RNA"
-        } ],
+        "comments" : [ "Binds TFIIB." ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "B-recognition element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "telomerase RNA",
+          "val" : "BREu motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "TFIIB recognition element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "BREu",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:telomerase_RNA",
+          "val" : "BRE motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "transcription factor B-recognition element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31484,13 +35758,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "telomerase_RNA"
+      "lbl" : "BREu_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001239",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000011",
       "meta" : {
+        "definition" : {
+          "val" : "A gene which can be transcribed, but will not be translated into a protein.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "minor TSS",
+          "val" : "non protein-coding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31499,20 +35777,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minor_TSS"
+      "lbl" : "non_protein_coding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000389",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000495",
       "meta" : {
         "definition" : {
-          "val" : "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021" ]
+          "val" : "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Spot_42_RNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "spot-42 RNA",
+          "val" : "three prime D spacer",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3'D-SPACER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31521,17 +35800,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "spot_42_RNA"
+      "lbl" : "three_prime_D_spacer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001236",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001342",
       "meta" : {
         "definition" : {
-          "val" : "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Isowyosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Nucleobase"
+          "val" : "RNAMOD:101"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "imG2",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31539,17 +35823,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "base"
+      "lbl" : "isowyosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001235",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001341",
       "meta" : {
         "definition" : {
-          "val" : "A region containing at least one unique origin of replication and a unique termination site.",
-          "xrefs" : [ "ISBN:0716719207" ]
+          "val" : "4_demethylwyosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Replicon_(genetics)"
+          "val" : "RNAMOD:100"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "4-demethylwyosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "imG-14",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "four demethylwyosine",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -31557,17 +35854,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "replicon"
+      "lbl" : "four_demethylwyosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000388",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000494",
       "meta" : {
         "definition" : {
-          "val" : "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036" ]
+          "val" : "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RRE RNA",
+          "val" : "three prime D nonamer",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3'D-NOMAMER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31576,17 +35877,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RRE_RNA"
+      "lbl" : "three_prime_D_nonamer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001238",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000010",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "major TSS",
+        "definition" : {
+          "val" : "A gene which, when transcribed, can be translated into a protein.",
           "xrefs" : [ ]
-        }, {
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "major transcription start site",
+          "val" : "protein-coding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31595,74 +35896,82 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "major_TSS"
+      "lbl" : "protein_coding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001237",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000013",
       "meta" : {
         "definition" : {
-          "val" : "A sequence feature that corresponds to a single amino acid residue in a polypeptide.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A small non coding RNA sequence, present in the cytoplasm.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Amino_acid"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "amino acid",
+          "val" : "small cytoplasmic RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:scRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Probably in the future this will cross reference to Chebi."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "amino_acid"
+      "lbl" : "scRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002124",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000497",
       "meta" : {
         "definition" : {
-          "val" : "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin_Diversity_ gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "immunoglobulin_D_gene",
+          "val" : "five prime D nonamer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IGD_gene",
+          "val" : "5'D-NONAMER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T15:59:10Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "IG_D_gene"
+      "lbl" : "five_prime_D_nonamer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001276",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001344",
       "meta" : {
+        "definition" : {
+          "val" : "5_methyluridine is a modified uridine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:052"
+        }, {
+          "val" : "http://en.wikipedia.org/wiki/5-methyluridine"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified guanosine",
+          "val" : "m5U",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five methyluridine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5-methyluridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31671,53 +35980,56 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_guanosine"
+      "lbl" : "five_methyluridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002125",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000012",
       "meta" : {
         "definition" : {
-          "val" : "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote.",
+          "xrefs" : [ "http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin_Joining_Gene",
+          "val" : "scRNA transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "small cytoplasmic RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "immunoglobulin_J_gene",
+          "val" : "small cytoplasmic RNA transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IG_joining_gene",
+          "val" : "scRNA primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "small_cytoplasmic_RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:00:36Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "IG_J_gene"
+      "lbl" : "scRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001275",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000496",
       "meta" : {
         "definition" : {
-          "val" : "A modified cytidine is a cytidine base feature which has been altered.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified cytidine",
+          "val" : "5'D-HEPTAMER",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime D heptamer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31726,28 +36038,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_cytidine"
+      "lbl" : "five_prime_D_heptamer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001278",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001343",
       "meta" : {
         "definition" : {
-          "val" : "1-methylinosine is a modified inosine.",
+          "val" : "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:018"
+          "val" : "RNAMOD:106"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "1-methylinosine",
-          "xrefs" : [ ]
+          "val" : "m2,7Gm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m1I",
+          "val" : "N2,7,2'-O-trimethylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "one methylinosine",
+          "val" : "N2 7 2prirme O trimethylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31756,81 +36069,67 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "one_methylinosine"
+      "lbl" : "N2_7_2prirme_O_trimethylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002122",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000491",
       "meta" : {
         "definition" : {
-          "val" : "A germline immunoglobulin  gene.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "All_IG_genes",
+          "val" : "VJ J cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IG_genes",
+          "val" : "(VJ)-J-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T15:56:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "immunoglobulin_gene"
+      "lbl" : "VJ_J_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002123",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000490",
       "meta" : {
         "definition" : {
-          "val" : "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin_Constant_germline_Gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "IGC_gene",
+          "val" : "VJ J C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "immunoglobulin_C_gene",
+          "val" : "(VJ)-J-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T15:57:29Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "IG_C_gene"
+      "lbl" : "VJ_J_C_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001277",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000493",
       "meta" : {
+        "definition" : {
+          "val" : "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified uridine",
+          "val" : "3'D-HEPTAMER",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "three prime D heptamer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31839,49 +36138,48 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_uridine"
+      "lbl" : "three_prime_D_heptamer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002120",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001340",
       "meta" : {
         "definition" : {
-          "val" : "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "1_2prime_O_dimethylguanosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:096"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3prime_overlapping_ncRNA",
+          "val" : "1,2'-O-dimethylguanosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "3'_overlapping_ncrna",
-          "xrefs" : [ ]
+          "val" : "m1Gm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "three prime overlapping noncoding rna",
+          "val" : "one two prime O dimethylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T15:48:21Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_overlapping_ncrna"
+      "lbl" : "one_two_prime_O_dimethylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001272",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000492",
       "meta" : {
+        "definition" : {
+          "val" : "Recombination signal including D-heptamer, D-spacer and D-nonamer in 5' of D-region of a D-gene or D-sequence.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tRNA gene",
+          "val" : "D gene recombination feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31890,41 +36188,67 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tRNA_gene"
+      "lbl" : "D_gene_recombination_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002121",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000008",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_sensu_your_favorite_organism"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001339",
       "meta" : {
         "definition" : {
-          "val" : "The configuration of the  IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements  (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci).",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "N2_N2_7_trimethylguanosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:091"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "immune_gene",
+          "val" : "m2,2,7G",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N2,N2,7-trimethylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T15:54:51Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immune_system_gene"
+      "lbl" : "N2_N2_7_trimethylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001271",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001338",
       "meta" : {
+        "definition" : {
+          "val" : "N2_7_dimethylguanosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:090"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tmRNA gene",
+          "val" : "m2,7G",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N2 7 dimethylguanosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N2,7-dimethylguanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31933,17 +36257,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tmRNA_gene"
+      "lbl" : "N2_7_dimethylguanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001274",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000007",
       "meta" : {
         "definition" : {
-          "val" : "A modified inosine is an inosine base feature that has been altered.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert.",
+          "xrefs" : [ "SO:ls" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified inosine",
+          "val" : "read-pair",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mate pair",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -31952,58 +36281,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_inosine"
+      "lbl" : "read_pair"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001273",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000009",
       "meta" : {
-        "definition" : {
-          "val" : "A modified adenine is an adenine base feature that has been altered.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "modified adenosine",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "modified_adenosine"
+      "lbl" : "gene_class"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002119",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000004",
       "meta" : {
         "definition" : {
-          "val" : "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A coding exon that is not the most 3-prime or the most 5-prime in a given transcript.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "WIKI:https://en.wikipedia.org/wiki/Allele_frequency"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-21T11:58:55Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by HL7 clinical genomics group."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "allelic_frequency"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001269",
-      "meta" : {
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SRP RNA gene",
+          "val" : "interior coding exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32012,72 +36312,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SRP_RNA_gene"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002117",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:27:21Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "<new term>"
+      "lbl" : "interior_coding_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002118",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000488",
       "meta" : {
         "definition" : {
-          "val" : "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "NMD polymorphic pseudogene transcript",
+          "val" : "(VDJ)-J-CLUSTER",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nonsense_mediated_decay_polymorphic_pseudogene",
+          "val" : "VDJ J cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:28:02Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "NMD_polymorphic_pseudogene_transcript"
+      "lbl" : "VDJ_J_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001268",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty",
+      "type" : "PROPERTY",
+      "lbl" : "subset_property"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001335",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a small nuclear RNA.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Small_nuclear_RNA" ]
+          "val" : "Undermodified_hydroxywybutosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:040"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA gene",
-          "xrefs" : [ ]
+          "val" : "OHyW*",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA gene",
+          "val" : "undermodified hydroxywybutosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32086,127 +36366,118 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "snRNA_gene"
+      "lbl" : "undermodified_hydroxywybutosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002115",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001334",
       "meta" : {
         "definition" : {
-          "val" : "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "Hydroxywybutosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:039"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pseudogene retained intron",
-          "xrefs" : [ ]
+          "val" : "OHyW",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:19:04Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudogenic_transcript_with_retained_intron"
+      "lbl" : "hydroxywybutosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002116",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000003",
       "meta" : {
         "definition" : {
-          "val" : "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/G-quadruplex"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polymorphic pseudogene processed transcript",
+          "val" : "G-quartet",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
+          "pred" : "hasExactSynonym",
+          "val" : "G_quadruplex",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:23:59Z"
+          "pred" : "hasExactSynonym",
+          "val" : "G tetrad",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "polymorphic_pseudogene_processed_transcript"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001265",
-      "meta" : {
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "stRNA_gene",
+          "val" : "G-quadruplex",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "stRNA gene",
+          "val" : "G quartet",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "miRNA gene",
+          "val" : "G-tetrad",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "guanine tetrad",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001270"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miRNA_gene"
+      "lbl" : "G_quartet"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002113",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000487",
       "meta" : {
         "definition" : {
-          "val" : "A lncRNA transcript containing a retained intron.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lncRNA_retained_intron",
+          "val" : "VDJ J C cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "lncRNA with retained intron",
+          "val" : "(VDJ)-J-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:13:07Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lncRNA_with_retained_intron"
+      "lbl" : "VDJ_J_C_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001264",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000006",
       "meta" : {
+        "definition" : {
+          "val" : "A region amplified by a PCR reaction.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/RAPD"
+        } ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "amplicon",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "gRNA gene",
+          "val" : "PCR product",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32215,80 +36486,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gRNA_gene"
+      "lbl" : "PCR_product"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002114",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001337",
       "meta" : {
         "definition" : {
-          "val" : "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "Methylwyosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "http://www.gencodegenes.org/gencode_biotypes.html"
+          "val" : "RNAMOD:042"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nonsense mediated decay transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "protein_coding_NMD",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "NMD transcript",
-          "xrefs" : [ ]
+          "val" : "mimG",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:16:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "NMD_transcript"
+      "lbl" : "methylwyosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002111",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000005",
       "meta" : {
         "definition" : {
-          "val" : "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus).",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Satellite_DNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pseudogene processed transcript",
+          "val" : "satellite DNA",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:07:00Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "pseudogene_processed_transcript"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001267",
-      "meta" : {
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snoRNA gene",
+          "val" : "INSDC_qualifier:satellite",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32297,42 +36540,45 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "snoRNA_gene"
+      "lbl" : "satellite_DNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002112",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000489",
       "meta" : {
         "definition" : {
-          "val" : "A protein coding transcript containing a retained intron.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "VJ C cluster",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mRNA with retained intron",
+          "val" : "(VJ)-C-CLUSTER",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T14:09:49Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_transcript_with_retained_intron"
+      "lbl" : "VJ_C_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001266",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001336",
       "meta" : {
+        "definition" : {
+          "val" : "Wyosine is a modified guanosine base feature.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+        },
+        "xrefs" : [ {
+          "val" : "RNAMOD:041"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "scRNA gene",
-          "xrefs" : [ ]
+          "val" : "IMG",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -32340,67 +36586,76 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "scRNA_gene"
+      "lbl" : "wyosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001261",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001254",
       "meta" : {
         "definition" : {
-          "val" : "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.",
+          "val" : "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "overlapping feature set",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Polyploid"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "overlapping_feature_set"
+      "lbl" : "polyploid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002110",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002102",
       "meta" : {
         "definition" : {
-          "val" : "A polymorphic  pseudogene in the reference genome, containing a retained intron,  known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polymorphic pseudogene with retained intron",
+          "val" : "IG_variable_pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Immunoglobulin variable pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "IG V pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "IG variable pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Immunoglobulin_variable_pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T12:47:33Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2016-07-15T16:05:56Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polymorphic_pseudogene_with_retained_intron"
+      "lbl" : "IG_V_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001260",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001253",
       "meta" : {
         "definition" : {
-          "val" : "A collection of discontinuous sequences.",
+          "val" : "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence collection",
+          "val" : "sonicate fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32409,41 +36664,58 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_collection"
+      "lbl" : "sonicate_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001263",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002103",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a non-coding RNA.",
-          "xrefs" : [ ]
+          "val" : "A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ncRNA gene",
+          "val" : "T_cell_receptor_Variable_pseudogene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non-coding RNA gene",
+          "val" : "T cell receptor V pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "T_cell_receptor_V_pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TR V pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "T cell receptor Variable pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-15T16:06:29Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ncRNA_gene"
+      "lbl" : "TR_V_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001262",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001256",
       "meta" : {
         "definition" : {
-          "val" : "A continous experimental result region extending the length of multiple overlapping EST's.",
+          "val" : "A polyploid where the multiple chromosome set was derived from a different organism.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "overlapping EST set",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Allopolyploid"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -32451,127 +36723,141 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "overlapping_EST_set"
+      "lbl" : "allopolyploid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002108",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002100",
       "meta" : {
         "definition" : {
-          "val" : "A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcribed unitary pseudogene",
+          "val" : "IG C pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-15T16:05:08Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T12:44:26Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcribed_unitary_pseudogene"
+      "lbl" : "IG_C_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002109",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001255",
       "meta" : {
         "definition" : {
-          "val" : "A processed_pseudogene overlapped by locus-specific evidence of transcription.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "A polyploid where the multiple chromosome set was derived from the same organism.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "transcribed processed pseudogene",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Autopolyploid"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T12:45:48Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcribed_processed_pseudogene"
+      "lbl" : "autopolyploid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002106",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002101",
       "meta" : {
         "definition" : {
-          "val" : "A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translated_nonprocessed_pseudogene",
+          "val" : "IG_joining_pseudogene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "translated unprocessed pseudogene",
+          "val" : "Immunoglobulin_Joining_Pseudogene",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T12:34:42Z"
+          "pred" : "hasExactSynonym",
+          "val" : "IG J pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "IG joining pseudogene",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Immunoglobulin Joining Pseudogene",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-15T16:05:34Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translated_unprocessed_pseudogene"
+      "lbl" : "IG_J_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001258",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001250",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.",
-          "xrefs" : [ "GOC:dh", "PMID:3095662" ]
+          "val" : "A fingerprint_map is a physical map composed of restriction fragments.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "octamer motif",
+          "val" : "BACmap",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "restriction map",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "fingerprint map",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "FPCmap",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "FPC",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Nature. 1986 Oct 16-22;323(6089):640-3."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "octamer_motif"
+      "lbl" : "fingerprint_map"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001257",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001252",
       "meta" : {
         "definition" : {
-          "val" : "The binding site (recognition site) of a homing endonuclease. The binding site is typically large.",
+          "val" : "A radiation hybrid map is a physical map.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "homing endonuclease binding site",
+          "val" : "RH map",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "radiation hybrid map",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32580,121 +36866,126 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "homing_endonuclease_binding_site"
+      "lbl" : "RH_map"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002107",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001251",
       "meta" : {
         "definition" : {
-          "val" : "A unprocessed pseudogene supported by locus-specific evidence of transcription.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "An STS map is a physical map organized by the unique STS landmarks.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcribed unprocessed pseudogene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "transcribed_non_processed_pseudogene",
+          "val" : "STS map",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T12:41:53Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcribed_unprocessed_pseudogene"
+      "lbl" : "STS_map"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002104",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001247",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "An oligo composed of synthetic nucleotides.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_J_pseudogene",
+          "val" : "synthetic oligo",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "synthetic_oligo"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_0000341",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001112"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000399",
+      "meta" : {
+        "definition" : {
+          "val" : "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/U12_snRNA"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TR J pseudogene",
-          "xrefs" : [ ]
+          "val" : "small nuclear RNA U12",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "T cell receptor J pseudogene",
-          "xrefs" : [ ]
+          "val" : "U12 small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_Joining_pseudogene",
-          "xrefs" : [ ]
+          "val" : "snRNA U12",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "T cell receptor Joining pseudogene",
+          "val" : "U12 snRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:06:51Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TR_J_pseudogene"
+      "lbl" : "U12_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002105",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001246",
       "meta" : {
         "definition" : {
-          "val" : "A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "The loop of the hairpin loop formed by folding of the pre-miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translated processed pseudogene",
+          "val" : "miRNA loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-18T12:31:53Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added as part of collaboration with Gencode, adding biotypes used in annotation."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translated_processed_pseudogene"
+      "lbl" : "miRNA_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001259",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001249",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in an apicoplast.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "apicoplast chromosome",
+          "val" : "physical map",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "fragment assembly",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32703,62 +36994,65 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "apicoplast_chromosome"
+      "lbl" : "fragment_assembly"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002146",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001248",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
-          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
+          "val" : "A region of the genome of known length that is composed by ordering and aligning two or more different regions.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "H2AZK7ac",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2AZK7 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2A.ZK7ac",
-          "xrefs" : [ ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T14:23:11Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2AZK7_acetylation_site"
+      "lbl" : "assembly"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001298",
+      "id" : "http://purl.obolibrary.org/obo/BS_0000340",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001119"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000396",
       "meta" : {
         "definition" : {
-          "val" : "2prime_O_methyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:004"
+          "val" : "http://en.wikipedia.org/wiki/U6_snRNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Am",
-          "xrefs" : [ ]
+          "val" : "U6 small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2'-O-methyladenosine",
+          "val" : "U6 snRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "two prime O methyladenosine",
-          "xrefs" : [ ]
+          "val" : "snRNA U6",
+          "xrefs" : [ "RSC:cb" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small nuclear RNA U6",
+          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -32766,62 +37060,53 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_prime_O_methyladenosine"
+      "lbl" : "U6_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002147",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001243",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
-          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
+          "val" : "A part of an miRNA primary_transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2AZK11 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2A.ZK11ac",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2AZK11ac",
+          "val" : "miRNA primary transcript region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T14:23:31Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2AZK11_acetylation_site"
+      "lbl" : "miRNA_primary_transcript_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001297",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000395",
       "meta" : {
         "definition" : {
-          "val" : "N6_methyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:003"
+          "val" : "http://en.wikipedia.org/wiki/U5_snRNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m6A",
-          "xrefs" : [ ]
+          "val" : "small nuclear RNA U5",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6-methyladenosine",
-          "xrefs" : [ ]
+          "val" : "U5 small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N6 methyladenosine",
+          "val" : "U5 snRNA",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snRNA U5",
+          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -32829,117 +37114,84 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_methyladenosine"
+      "lbl" : "U5_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002144",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001242",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001021"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000398",
       "meta" : {
         "definition" : {
-          "val" : "A histone 2AZ modification where the modification is the acetylation of the residue.",
-          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
+          "val" : "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence.",
+          "xrefs" : [ "PMID:9622129" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/U11_snRNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2AZac",
-          "xrefs" : [ ]
+          "val" : "snRNA U11",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "histone 2AZ acetylation site",
+          "val" : "U11 snRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2A.Zac",
-          "xrefs" : [ ]
+          "val" : "small nuclear RNA U11",
+          "xrefs" : [ "RSC:cb" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U11 small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T14:11:49Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histone_2AZ_acetylation_site"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#translates_to",
-      "meta" : {
-        "definition" : {
-          "val" : "Inverse of translation _of.",
-          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: codon translates_to amino_acid."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T12:11:53Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "translates_to"
+      "lbl" : "U11_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002145",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001245",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
-          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
+          "val" : "The stem of the hairpin loop formed by folding of the pre-miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2AZK4 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2AZK4ac",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2A.ZK4ac",
+          "val" : "miRNA stem",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T14:19:43Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2AZK4_acetylation_site"
+      "lbl" : "miRNA_stem"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001299",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001244",
       "meta" : {
         "definition" : {
-          "val" : "2_methylthio_N6_methyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:005"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "two methylthio N6 methyladenosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ms2m6A",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "2-methylthio-N6-methyladenosine",
+          "val" : "pre-miRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -32948,53 +37200,61 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_methylthio_N6_methyladenosine"
+      "lbl" : "pre_miRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002142",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000397",
       "meta" : {
         "definition" : {
-          "val" : "A histone 2A modification where the modification is the acetylation of the residue.",
-          "xrefs" : [ "ISBN:0815341059" ]
+          "val" : "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394).",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histone 2A acetylation site",
-          "xrefs" : [ ]
+          "val" : "U6atac snRNA",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2Aac",
-          "xrefs" : [ ]
+          "val" : "U6atac small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snRNA U6atac",
+          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T12:03:46Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histone_2A_acetylation_site"
+      "lbl" : "U6atac_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001294",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000392",
       "meta" : {
         "definition" : {
-          "val" : "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:107"
+          "val" : "http://en.wikipedia.org/wiki/U2_snRNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N4,N4,2'-O-trimethylcytidine",
-          "xrefs" : [ ]
+          "val" : "snRNA U2",
+          "xrefs" : [ "RSC:CB" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m42Cm",
+          "val" : "U2 small nuclear RNA",
+          "xrefs" : [ "RSC:CB" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small nuclear RNA U2",
+          "xrefs" : [ "RSC:CB" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U2 snRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33003,29 +37263,34 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N4_N4_2_prime_O_trimethylcytidine"
+      "lbl" : "U2_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001293",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000391",
       "meta" : {
         "definition" : {
-          "val" : "5-formyl-2'-O-methylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:095"
+          "val" : "http://en.wikipedia.org/wiki/U1_snRNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five formyl two prime O methylcytidine",
-          "xrefs" : [ ]
+          "val" : "snRNA U1",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-formyl-2'-O-methylcytidine",
-          "xrefs" : [ ]
+          "val" : "U1 small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "f5Cm",
+          "val" : "U1 snRNA",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small nuclear RNA U1",
+          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -33033,91 +37298,85 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_formyl_two_prime_O_methylcytidine"
+      "lbl" : "U1_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002143",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001241",
       "meta" : {
         "definition" : {
-          "val" : "A histone 2B modification where the modification is the acetylation of the residue.",
-          "xrefs" : [ "ISBN:0815341059" ]
+          "val" : "A gene that has multiple possible transcription start sites.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histone 2B acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2Bac",
+          "val" : "encodes alternate transcription start sites",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T12:04:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histone_2B_acetylation_site"
+      "lbl" : "encodes_alternate_transcription_start_sites"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002140",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000394",
       "meta" : {
         "definition" : {
-          "val" : "An origin of replication that initiates early in S phase.",
-          "xrefs" : [ "PMID:23348837", "PMID:9115207" ]
+          "val" : "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397).",
+          "xrefs" : [ "PMID:12409455" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "early replication origin",
+          "val" : "U4atac snRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "early origin",
-          "xrefs" : [ ]
+          "val" : "snRNA U4atac",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "early origin of replication",
-          "xrefs" : [ ]
+          "val" : "small nuclear RNA U4atac",
+          "xrefs" : [ "RSC:cb" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U4atac small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-09-15T15:53:36Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "early_origin_of_replication"
+      "lbl" : "U4atac_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001296",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000393",
       "meta" : {
         "definition" : {
-          "val" : "2_methyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:002"
+          "val" : "http://en.wikipedia.org/wiki/U4_snRNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m2A",
-          "xrefs" : [ ]
+          "val" : "small nuclear RNA U4",
+          "xrefs" : [ "RSC:cb" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2-methyladenosine",
+          "val" : "U4 snRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "two methyladenosine",
-          "xrefs" : [ ]
+          "val" : "U4 small nuclear RNA",
+          "xrefs" : [ "RSC:cb" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snRNA U4",
+          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -33125,61 +37384,53 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_methyladenosine"
+      "lbl" : "U4_snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002141",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001240",
       "meta" : {
         "definition" : {
-          "val" : "An origin of replication that initiates late in S phase.",
-          "xrefs" : [ "PMID:23348837", "PMID:9115207" ]
+          "val" : "The region of a gene from the 5' most TSS to the 3' TSS.",
+          "xrefs" : [ "BBOP:nw" ]
         },
+        "comments" : [ "Merged into promoter (SO:0000167) on 11 Feb 2021 by Dave Sant. GREEKC had asked us to merge these terms to reduce redundancy. See GitHub Issue #528" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "late origin of replication",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "late origin",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "late replication origin",
+          "val" : "TSS region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-09-15T15:56:07Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0000167"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "late_origin_of_replication"
+      "lbl" : "TSS_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001295",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000390",
       "meta" : {
         "definition" : {
-          "val" : "1_methyladenosine is a modified adenosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:001"
+          "val" : "http://en.wikipedia.org/wiki/Telomerase_RNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m1A",
+          "val" : "telomerase RNA",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "one methyladenosine",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "1-methyladenosine",
+          "val" : "INSDC_qualifier:telomerase_RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33188,28 +37439,43 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "one_methyladenosine"
+      "lbl" : "telomerase_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001290",
+      "id" : "http://purl.obolibrary.org/obo/BS_0000338",
       "meta" : {
-        "definition" : {
-          "val" : "N4-methylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
-        },
-        "xrefs" : [ {
-          "val" : "RNAMOD:082"
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001079"
         } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "N4-methylcytidine",
-          "xrefs" : [ ]
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_0000339",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001116"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m4C",
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001239",
+      "meta" : {
+        "definition" : {
+          "val" : "A tanscription start site that is not the most frequently used for transcription of a gene.",
           "xrefs" : [ ]
-        }, {
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N4 methylcytidine",
+          "val" : "minor TSS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33218,29 +37484,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N4_methylcytidine"
+      "lbl" : "minor_TSS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001292",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001236",
       "meta" : {
         "definition" : {
-          "val" : "5-hydroxymethylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "RNAMOD:084"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "five hydroxymethylcytidine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "hm5C",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5-hydroxymethylcytidine",
-          "xrefs" : [ ]
+          "val" : "http://en.wikipedia.org/wiki/Nucleobase"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -33248,28 +37502,39 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_hydroxymethylcytidine"
+      "lbl" : "base"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001291",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000389",
       "meta" : {
         "definition" : {
-          "val" : "N4,2'-O-dimethylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:083"
+          "val" : "http://en.wikipedia.org/wiki/Spot_42_RNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m4Cm",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N4 2 prime O dimethylcytidine",
+          "val" : "spot-42 RNA",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "spot_42_RNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000388",
+      "meta" : {
+        "definition" : {
+          "val" : "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N4,2'-O-dimethylcytidine",
+          "val" : "RRE RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33278,197 +37543,200 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N4_2_prime_O_dimethylcytidine"
+      "lbl" : "RRE_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002139",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001235",
       "meta" : {
         "definition" : {
-          "val" : "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "A region containing at least one unique origin of replication and a unique termination site.",
+          "xrefs" : [ "ISBN:0716719207" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Replicon_(genetics)"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "replicon"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001238",
+      "meta" : {
+        "definition" : {
+          "val" : "The tanscription start site that is most frequently used for transcription of a gene.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TEC",
+          "val" : "major transcription start site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "to_be_experimentally_confirmed_transcript",
+          "val" : "major TSS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:28:07Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unconfirmed_transcript"
+      "lbl" : "major_TSS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002137",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001237",
       "meta" : {
         "definition" : {
-          "val" : "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "A sequence feature that corresponds to a single amino acid residue in a polypeptide.",
+          "xrefs" : [ "RSC:cb" ]
         },
+        "comments" : [ "Probably in the future this will cross reference to Chebi." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Amino_acid"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_V_gene",
+          "val" : "amino acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:21:04Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TR_V_Gene"
+      "lbl" : "amino_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002138",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001276",
       "meta" : {
         "definition" : {
-          "val" : "A transcript feature that has been predicted but is not yet validated.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A guanosine base that has been modified.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "predicted transcript",
+          "val" : "modified guanosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:27:38Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "predicted_transcript"
+      "lbl" : "modified_guanosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001287",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002124",
       "meta" : {
         "definition" : {
-          "val" : "5,2'-O-dimethylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:026"
-        } ],
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m5Cm",
+          "val" : "immunoglobulin_D_gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five two prime O dimethylcytidine",
+          "val" : "IGD_gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5,2'-O-dimethylcytidine",
+          "val" : "Immunoglobulin_Diversity_ gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T15:59:10Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_two_prime_O_dimethylcytidine"
+      "lbl" : "IG_D_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002135",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002125",
       "meta" : {
         "definition" : {
-          "val" : "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene.",
+          "val" : "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.",
           "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_D_gene",
+          "val" : "immunoglobulin_J_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Immunoglobulin_Joining_Gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "IG_joining_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:20:06Z"
+          "val" : "2016-08-23T16:00:36Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TR_D_Gene"
+      "lbl" : "IG_J_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002136",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001275",
       "meta" : {
         "definition" : {
-          "val" : "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "A modified cytidine is a cytidine base feature which has been altered.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_J_gene",
+          "val" : "modified cytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:20:36Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TR_J_Gene"
+      "lbl" : "modified_cytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001286",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001278",
       "meta" : {
         "definition" : {
-          "val" : "5-formylcytidine is a modified cytidine.",
+          "val" : "1-methylinosine is a modified inosine.",
           "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "RNAMOD:025"
+          "val" : "RNAMOD:018"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five formylcytidine",
+          "val" : "one methylinosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "f5C",
+          "val" : "1-methylinosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-formylcytidine",
-          "xrefs" : [ ]
+          "val" : "m1I",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -33476,50 +37744,47 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_formylcytidine"
+      "lbl" : "one_methylinosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002133",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002122",
       "meta" : {
         "definition" : {
-          "val" : "A T-cell receptor germline gene.",
-          "xrefs" : [ ]
+          "val" : "A germline immunoglobulin gene.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TR_gene",
+          "val" : "IG_genes",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "All_IG_genes",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:17:12Z"
+          "val" : "2016-08-23T15:56:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "T_cell_receptor_gene"
+      "lbl" : "immunoglobulin_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001289",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001277",
       "meta" : {
         "definition" : {
-          "val" : "Lysidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A uridine base that has been modified.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:028"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Lysidine"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "k2C",
+          "val" : "modified uridine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33528,193 +37793,151 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lysidine"
+      "lbl" : "modified_uridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001288",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002123",
       "meta" : {
         "definition" : {
-          "val" : "N4-acetyl-2'-O-methylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:027"
-        } ],
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N4 acetyl 2 prime O methylcytidine",
+          "val" : "Immunoglobulin_Constant_germline_Gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "N4-acetyl-2'-O-methylcytidine",
+          "val" : "IGC_gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ac4Cm",
+          "val" : "immunoglobulin_C_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T15:57:29Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N4_acetyl_2_prime_O_methylcytidine"
+      "lbl" : "IG_C_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002134",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001272",
       "meta" : {
         "definition" : {
-          "val" : "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "A noncoding RNA that binds to a specific amino acid to allow that amino acid to be used by the ribosome during translation of RNA.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T_cell_receptor_C_gene",
+          "val" : "tRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:19:20Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TR_C_Gene"
+      "lbl" : "tRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002131",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002120",
       "meta" : {
         "definition" : {
-          "val" : "A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence.",
-          "xrefs" : [ "GENECODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sense_intronic_lncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sense_intronic_non-coding_RNA",
+          "val" : "3'_overlapping_ncrna",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sense intronic lncRNA",
+          "val" : "three prime overlapping noncoding rna",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sense_intronic",
+          "val" : "3prime_overlapping_ncRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:15:02Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001903"
+          "val" : "2016-08-23T15:48:21Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sense_intronic_ncRNA"
+      "lbl" : "three_prime_overlapping_ncrna"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001283",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002121",
       "meta" : {
         "definition" : {
-          "val" : "2'-O-methylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci).",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:022"
-        } ],
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "2'-O-methylcytidine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Cm",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "two prime O methylcytidine",
+          "val" : "immune_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T15:54:51Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_prime_O_methylcytidine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#VAR",
-      "type" : "PROPERTY",
-      "lbl" : "variant annotation term"
+      "lbl" : "vertebrate_immune_system_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002132",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001271",
       "meta" : {
         "definition" : {
-          "val" : "A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence.",
-          "xrefs" : [ "GENECODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "A bacterial RNA with both tRNA and mRNA like properties.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sense_overlap_lncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sense overlap lncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sense_overlapping",
+          "val" : "tmRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:16:13Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sense_overlap_ncRNA"
+      "lbl" : "tmRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001282",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001274",
       "meta" : {
         "definition" : {
-          "val" : "5-methylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A modified inosine is an inosine base feature that has been altered.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:021"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five methylcytidine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m5C",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5-methylcytidine",
+          "val" : "modified inosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33723,28 +37946,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_methylcytidine"
+      "lbl" : "modified_inosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001285",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001273",
       "meta" : {
         "definition" : {
-          "val" : "N4-acetylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A modified adenine is an adenine base feature that has been altered.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:024"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "N4-acetylcytidine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ac4C",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N4 acetylcytidine",
+          "val" : "modified adenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33753,53 +37965,71 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N4_acetylcytidine"
+      "lbl" : "modified_adenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002130",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001270",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001265"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002119",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that contains a CDS but has no stop codon before the polyA site is reached.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "non_stop_decay_transcript",
-          "xrefs" : [ ]
+        "comments" : [ "Requested by HL7 clinical genomics group." ],
+        "xrefs" : [ {
+          "val" : "WIKI:https://en.wikipedia.org/wiki/Allele_frequency"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:11:34Z"
+          "val" : "2016-07-21T11:58:55Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "NSD_transcript"
+      "lbl" : "allelic_frequency"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001284",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002117",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T14:27:21Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "<new term>"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001269",
       "meta" : {
         "definition" : {
-          "val" : "2-thiocytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A gene that encodes a signal recognition particle (SRP) RNA.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:023"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "s2C",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "two thiocytidine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "2-thiocytidine",
+          "val" : "SRP RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33808,58 +38038,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_thiocytidine"
+      "lbl" : "SRP_RNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001281",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002118",
       "meta" : {
         "definition" : {
-          "val" : "3-methylcytidine is a modified cytidine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:020"
-        } ],
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m3C",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "3-methylcytidine",
+          "val" : "nonsense_mediated_decay_polymorphic_pseudogene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "three methylcytidine",
+          "val" : "NMD polymorphic pseudogene transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T14:28:02Z"
+        } ]
+      },
       "type" : "CLASS",
-      "lbl" : "three_methylcytidine"
+      "lbl" : "NMD_polymorphic_pseudogene_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001280",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001268",
       "meta" : {
         "definition" : {
-          "val" : "2'-O-methylinosine is a modified inosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A gene that encodes a small nuclear RNA.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Small_nuclear_RNA" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:081"
-        } ],
+        "comments" : [ "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Im",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "two prime O methylinosine",
+          "val" : "snRNA gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2'-O-methylinosine",
+          "val" : "small nuclear RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -33868,841 +38092,759 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "two_prime_O_methylinosine"
+      "lbl" : "snRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002128",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002115",
       "meta" : {
         "definition" : {
-          "val" : "Mitochondrial ribosomal RNA.",
+          "val" : "A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence.",
           "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Mt_rRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mitochondrial_rRNA",
+          "val" : "pseudogene retained intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:08:59Z"
+          "val" : "2016-07-18T14:19:04Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mt_rRNA"
+      "lbl" : "pseudogenic_transcript_with_retained_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002129",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002116",
       "meta" : {
         "definition" : {
-          "val" : "Mitochondrial transfer RNA.",
+          "val" : "A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding.",
           "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mitochondrial_tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Mt_tRNA",
+          "val" : "polymorphic pseudogene processed transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:10:17Z"
+          "val" : "2016-07-18T14:23:59Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mt_tRNA"
+      "lbl" : "polymorphic_pseudogene_processed_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001279",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001265",
       "meta" : {
         "definition" : {
-          "val" : "1,2'-O-dimethylinosine is a modified inosine.",
-          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A small noncoding RNA of approximately 22 nucleotides in length which may be involved in regulation of gene expression.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:019"
-        } ],
+        "comments" : [ "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "1,2'-O-dimethylinosine",
+          "val" : "miRNA gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m'Im",
+          "val" : "stRNA gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "one two prime O dimethylinosine",
+          "val" : "stRNA_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001270"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "one_two_prime_O_dimethylinosine"
+      "lbl" : "miRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002126",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002113",
       "meta" : {
         "definition" : {
-          "val" : "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain.",
-          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
+          "val" : "A lncRNA transcript containing a retained intron.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "IG_variable_gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Immunoglobulin_variable_gene",
+          "val" : "lncRNA_retained_intron",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "IGV_gene",
+          "val" : "lncRNA with retained intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:02:09Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T14:13:07Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "IG_V_gene"
+      "lbl" : "lncRNA_with_retained_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002127",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002114",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a long non-coding RNA.",
+          "val" : "A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay.",
           "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
+        "xrefs" : [ {
+          "val" : "http://www.gencodegenes.org/gencode_biotypes.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lnc_RNA_gene",
+          "val" : "protein_coding_NMD",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "lnc RNA gene",
+          "val" : "nonsense mediated decay transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "long_non_coding_RNA_gene",
+          "val" : "NMD transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-08-23T16:03:33Z"
+          "val" : "2016-07-18T14:16:13Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes."
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lncRNA_gene"
+      "lbl" : "NMD_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002168",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001264",
       "meta" : {
         "definition" : {
-          "val" : "An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression.",
-          "xrefs" : [ "PMID:22421878" ]
+          "val" : "A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "https://en.wikipedia.org/wiki/RNA_thermometer"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA thermoregulator",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RNAT",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "thermoregulator",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RNA thermometer",
+          "val" : "gRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-07-17T10:07:45Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_thermometer"
+      "lbl" : "gRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002169",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002111",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17).",
-          "xrefs" : [ ]
+          "val" : "A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus).",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice polypyrimidine tract variant",
+          "val" : "pseudogene processed transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-07-31T13:40:13Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T14:07:00Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_polypyrimidine_tract_variant"
+      "lbl" : "pseudogene_processed_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002166",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001267",
       "meta" : {
         "definition" : {
-          "val" : "A ref_miRNA (RefSeq-miRNA) sequence is assigned at the creation of a new mature miRNA entry in a database. The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA.",
-          "xrefs" : [ "PMID:26453491" ]
+          "val" : "A gene encoding a small noncoding RNA that participates in the processing or chemical modifications of many RNAs, including ribosomal RNAs and spliceosomal RNAs.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514. Added additional children of snoRNA on 18 Nov 2021 at the request of Steven Marygold. See GitHub Issue #519." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ref miRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RefSeq-miRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RefSeq miRNA",
+          "val" : "snoRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-06-22T11:05:49Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ref_miRNA"
+      "lbl" : "snoRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002167",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002112",
       "meta" : {
         "definition" : {
-          "val" : "IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA.",
-          "xrefs" : [ "PMID:26453491" ]
+          "val" : "A protein coding transcript containing a retained intron.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mRNA with retained intron",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T14:09:49Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-06-22T11:09:42Z"
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "isomiR"
+      "lbl" : "coding_transcript_with_retained_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002164",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001266",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated.",
-          "xrefs" : [ "PMID:18552846", "http://www.actrec.gov.in/histome/ptm_sp.php?ptm_sp=H2BK5ac" ]
+          "val" : "A gene encoding a small noncoding RNA that is generally found only in the cytoplasm.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK5ac",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2BK5 acetylation site",
+          "val" : "scRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-05-17T15:22:58Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2BK5_acetylation_site"
+      "lbl" : "scRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002165",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001261",
       "meta" : {
         "definition" : {
-          "val" : "A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence.",
-          "xrefs" : [ ]
+          "val" : "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "trinucleotide repeat expansion",
+          "val" : "overlapping feature set",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-06-02T10:43:42Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trinucleotide_repeat_expansion"
+      "lbl" : "overlapping_feature_set"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002162",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002110",
       "meta" : {
         "definition" : {
-          "val" : "A short tandem repeat variant containing more repeat units than the reference sequence.",
-          "xrefs" : [ ]
+          "val" : "A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "short tandem repeat expansion",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "str expansion",
+          "val" : "polymorphic pseudogene with retained intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T12:47:33Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-04-26T12:51:26Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "short_tandem_repeat_expansion"
+      "lbl" : "polymorphic_pseudogene_with_retained_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002163",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001260",
       "meta" : {
         "definition" : {
-          "val" : "A short tandem repeat variant containing fewer repeat units than the reference sequence.",
-          "xrefs" : [ ]
+          "val" : "A collection of discontinuous sequences.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "short tandem repeat contraction",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "str contraction",
+          "val" : "sequence collection",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-04-26T12:52:33Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "short_tandem_repeat_contraction"
+      "lbl" : "sequence_collection"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002160",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001263",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the length of one or more sequence features.",
+          "val" : "A gene that encodes a non-coding RNA.",
           "xrefs" : [ ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#Alliance_of_Genome_Resources" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence length variant",
+          "val" : "ncRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non-coding RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-04-26T12:31:12Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_length_variant"
+      "lbl" : "ncRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002161",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001262",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded.",
-          "xrefs" : [ ]
+          "val" : "A continous experimental result region extending the length of multiple overlapping EST's.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "str change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "short tandem repeat change",
+          "val" : "overlapping EST set",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-04-26T12:50:55Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "short_tandem_repeat_change"
+      "lbl" : "overlapping_EST_set"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#part_of",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002108",
       "meta" : {
         "definition" : {
-          "val" : "X part_of Y if X is a subregion of Y.",
-          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
+          "val" : "A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transcribed unitary pseudogene",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: amino_acid part_of polypeptide."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "part_of"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#member_of",
-      "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444."
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T12:44:26Z"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "member_of"
+      "type" : "CLASS",
+      "lbl" : "transcribed_unitary_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002159",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002109",
       "meta" : {
         "definition" : {
-          "val" : "A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence FXGKGX[RK]LG.",
-          "xrefs" : [ "PMID:17083136", "PMID:27655872" ]
+          "val" : "A processed_pseudogene overlapped by locus-specific evidence of transcription.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SHP box",
+          "val" : "transcribed processed pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-12-15T09:48:38Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T12:45:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SHP_box"
+      "lbl" : "transcribed_processed_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002157",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002106",
       "meta" : {
         "definition" : {
-          "val" : "A gene cassette array containing H+ mating type specific information.",
-          "xrefs" : [ "PMID:18354497" ]
+          "val" : "A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "translated_nonprocessed_pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "translated unprocessed pseudogene",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-18T12:34:42Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-11-17T10:59:00Z"
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Mat2P"
+      "lbl" : "translated_unprocessed_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002158",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001258",
       "meta" : {
         "definition" : {
-          "val" : "A gene cassette array containing H- mating type specific information.",
-          "xrefs" : [ "PMID:18354497" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors.",
+          "xrefs" : [ "GOC:dh", "PMID:3095662" ]
         },
+        "comments" : [ "Nature. 1986 Oct 16-22;323(6089):640-3." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "octamer motif",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-11-17T11:02:27Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Mat3M"
+      "lbl" : "octamer_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002155",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002107",
       "meta" : {
         "definition" : {
-          "val" : "A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase.",
-          "xrefs" : [ "NCBI:cf", "SO:ke" ]
+          "val" : "A unprocessed pseudogene supported by locus-specific evidence of transcription.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:meiotic_recombination",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:meiotic",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_recomb",
+          "val" : "transcribed_non_processed_pseudogene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "meiotic recombination region",
+          "val" : "transcribed unprocessed pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-28T10:34:55Z"
+          "val" : "2016-07-18T12:41:53Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "meiotic_recombination_region"
+      "lbl" : "transcribed_unprocessed_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002156",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001257",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'.",
-          "xrefs" : [ "PMID:1748287", "PMID:7623803" ]
+          "val" : "The binding site (recognition site) of a homing endonuclease. The binding site is typically large.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CArG box",
+          "val" : "homing endonuclease binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-28T10:42:06Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Antonia Lock"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CArG_box"
+      "lbl" : "homing_endonuclease_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002153",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002104",
       "meta" : {
         "definition" : {
-          "val" : "A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms.",
-          "xrefs" : [ "NCBI:dm", "SO:ke" ]
+          "val" : "A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "genic 5 prime transcript variant",
+          "val" : "TR J pseudogene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "genic upstream transcript variant",
+          "val" : "T_cell_receptor_J_pseudogene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "genic 5' transcript variant",
+          "val" : "T_cell_receptor_Joining_pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "T cell receptor Joining pseudogene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "T cell receptor J pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-28T10:23:17Z"
+          "val" : "2016-07-15T16:06:51Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "genic_upstream_transcript_variant"
+      "lbl" : "TR_J_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002154",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002105",
       "meta" : {
         "definition" : {
-          "val" : "A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells.",
-          "xrefs" : [ "NCBI:cf", "SO:ke" ]
+          "val" : "A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Term added as part of collaboration with Gencode, adding biotypes used in annotation." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:mitotic_recombination",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:mitotic",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_recomb",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mitotic recombination region",
+          "val" : "translated processed pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-28T10:33:54Z"
+          "val" : "2016-07-18T12:31:53Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mitotic_recombination_region"
+      "lbl" : "translated_processed_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002151",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001259",
       "meta" : {
         "definition" : {
-          "val" : "A uORF beginning with a codon other than AUG.",
-          "xrefs" : [ "PMID:26684391", "PMID:27313038" ]
+          "val" : "A chromosome originating in an apicoplast.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non AUG initiated uORF",
+          "val" : "apicoplast chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-26T09:37:45Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_AUG_initiated_uORF"
+      "lbl" : "apicoplast_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002152",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001298",
       "meta" : {
         "definition" : {
-          "val" : "A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms.",
-          "xrefs" : [ "NCBI:dm", "SO:ke" ]
+          "val" : "2prime_O_methyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:004"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "genic downstream transcript variant",
+          "val" : "two prime O methyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "genic 3' transcript variant",
-          "xrefs" : [ ]
+          "val" : "Am",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "genic 3 prime transcript variant",
+          "val" : "2'-O-methyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-28T10:20:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "genic_downstream_transcript_variant"
+      "lbl" : "two_prime_O_methyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002150",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002146",
       "meta" : {
         "definition" : {
-          "val" : "A uORF beginning with the canonical start codon AUG.",
-          "xrefs" : [ "PMID:26684391", "PMID:27313038" ]
+          "val" : "A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
+          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "AUG initiated uORF",
+          "val" : "H2A.ZK7ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2AZK7ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2AZK7 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-26T09:37:11Z"
+          "val" : "2016-10-25T14:23:11Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "AUG_initiated_uORF"
+      "lbl" : "H2AZK7_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_2000061",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002147",
       "meta" : {
         "definition" : {
-          "val" : "The sequence referred to by an entry in a databank such as GenBank or SwissProt.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
+          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "databank entry",
+          "val" : "H2AZK11 acetylation site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "accession",
+          "pred" : "hasExactSynonym",
+          "val" : "H2AZK11ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2A.ZK11ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-25T14:23:31Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "databank_entry"
+      "lbl" : "H2AZK11_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002148",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001297",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
-          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
+          "val" : "N6_methyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:003"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2A.ZK13ac",
+          "val" : "N6-methyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2AZK13 acetylation site",
-          "xrefs" : [ ]
+          "val" : "m6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2AZK13ac",
+          "val" : "N6 methyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T14:23:50Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2AZK13_acetylation_site"
+      "lbl" : "N6_methyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002149",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002144",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
+          "val" : "A histone 2AZ modification where the modification is the acetylation of the residue.",
           "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2AZK15ac",
+          "val" : "H2A.Zac",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2AZK15 acetylation site",
+          "val" : "histone 2AZ acetylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2A.ZK15ac",
+          "val" : "H2AZac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -34710,108 +38852,113 @@
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-10-25T14:24:08Z"
+          "val" : "2016-10-25T14:11:49Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2AZK15_acetylation_site"
+      "lbl" : "histone_2AZ_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#translation_of",
+      "id" : "http://purl.obolibrary.org/obo/so#translates_to",
       "meta" : {
         "definition" : {
-          "val" : "X is translation of Y if Y is translated by ribosome to create X.",
+          "val" : "Inverse of translation _of.",
           "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
+        "comments" : [ "Example: codon translates_to amino_acid." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: Polypeptide translation_of CDS."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T12:09:59Z"
+          "val" : "2009-08-19T12:11:53Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "PROPERTY",
-      "lbl" : "translation_of"
+      "lbl" : "translates_to"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002188",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002145",
       "meta" : {
         "definition" : {
-          "val" : "A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product.",
-          "xrefs" : [ "Clingen:mb" ]
+          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
+          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "functional gene region",
+          "val" : "H2A.ZK4ac",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-12-15T11:08:43Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors."
+          "pred" : "hasExactSynonym",
+          "val" : "H2AZK4 acetylation site",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2AZK4ac",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-25T14:19:43Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "functional_gene_region"
+      "lbl" : "H2AZK4_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002189",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001299",
       "meta" : {
         "definition" : {
-          "val" : "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.",
-          "xrefs" : [ ]
+          "val" : "2_methylthio_N6_methyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:005"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:gene",
-          "xrefs" : [ ]
+          "pred" : "hasExactSynonym",
+          "val" : "ms2m6A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:allelic",
+          "val" : "two methylthio N6 methyladenosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "allelic pseudogene",
+          "val" : "2-methylthio-N6-methyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-03T15:47:32Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "allelic_pseudogene"
+      "lbl" : "two_methylthio_N6_methyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002186",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002142",
       "meta" : {
         "definition" : {
-          "val" : "A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance.",
-          "xrefs" : [ ]
+          "val" : "A histone 2A modification where the modification is the acetylation of the residue.",
+          "xrefs" : [ "ISBN:0815341059" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mutational hotspot",
+          "val" : "H2Aac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "histone 2A acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -34819,294 +38966,336 @@
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-11-07T12:27:51Z"
+          "val" : "2016-10-25T12:03:46Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutational_hotspot"
+      "lbl" : "histone_2A_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002187",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001294",
       "meta" : {
         "definition" : {
-          "val" : "An insertion of sequence from the HERV family of mobile elements with respect to a reference.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:107"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "HERV insertion",
+          "val" : "m42Cm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N4,N4,2'-O-trimethylcytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-11-20T11:52:51Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "HERV_insertion"
+      "lbl" : "N4_N4_2_prime_O_trimethylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002184",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002143",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a sense intronic long non-coding RNA.",
-          "xrefs" : [ ]
+          "val" : "A histone 2B modification where the modification is the acetylation of the residue.",
+          "xrefs" : [ "ISBN:0815341059" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sense intronic ncRNA gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sense_intronic_lncRNA_gene",
+          "val" : "H2Bac",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sense intronic lncRNA gene",
+          "val" : "histone 2B acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-09-27T11:03:50Z"
+          "val" : "2016-10-25T12:04:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sense_intronic_ncRNA_gene"
+      "lbl" : "histone_2B_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002185",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001293",
       "meta" : {
         "definition" : {
-          "val" : "A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand.",
-          "xrefs" : [ "https://www.gencodegenes.org/gencode_biotypes.html" ]
+          "val" : "5-formyl-2'-O-methylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:095"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bidirectional promoter lncRNA",
+          "val" : "5-formyl-2'-O-methylcytidine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five formyl two prime O methylcytidine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "f5Cm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-10-03T11:43:48Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bidirectional_promoter_lncRNA"
+      "lbl" : "five_formyl_two_prime_O_methylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002182",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001296",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes an antisense long, non-coding RNA.",
-          "xrefs" : [ ]
+          "val" : "2_methyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:002"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "antisense lncRNA gene",
+          "val" : "two methyladenosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "2-methyladenosine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m2A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-09-27T10:44:00Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "antisense_lncRNA_gene"
+      "lbl" : "two_methyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002183",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002140",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a sense overlap long non-coding RNA.",
-          "xrefs" : [ ]
+          "val" : "An origin of replication that initiates early in S phase.",
+          "xrefs" : [ "PMID:23348837", "PMID:9115207" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sense overlap lncRNA gene",
+          "val" : "early origin",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sense overlap ncRNA gene",
+          "val" : "early replication origin",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sense_overlap_lncRNA_gene",
+          "val" : "early origin of replication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-09-15T15:53:36Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-09-27T10:48:05Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sense_overlap_ncRNA_gene"
+      "lbl" : "early_origin_of_replication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002180",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001295",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes an enzymatic RNA.",
-          "xrefs" : [ ]
+          "val" : "1_methyladenosine is a modified adenosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:001"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "enzymatic RNA gene",
+          "val" : "one methyladenosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m1A",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "1-methyladenosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-09-27T10:30:27Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "enzymatic_RNA_gene"
+      "lbl" : "one_methyladenosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002181",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002141",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a ribozyme.",
-          "xrefs" : [ ]
+          "val" : "An origin of replication that initiates late in S phase.",
+          "xrefs" : [ "PMID:23348837", "PMID:9115207" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ribozyme gene",
+          "val" : "late origin",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "late origin of replication",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "late replication origin",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-09-15T15:56:07Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-09-27T10:31:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ribozyme_gene"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/IAO_0000115",
-      "type" : "PROPERTY",
-      "lbl" : "definition"
+      "lbl" : "late_origin_of_replication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002179",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001290",
       "meta" : {
         "definition" : {
-          "val" : "An MNV that is the result of base-calling or assembly error.",
-          "xrefs" : [ ]
+          "val" : "N4-methylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:082"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "MNV artifact",
+          "val" : "m4C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N4-methylcytidine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N4 methylcytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T15:27:21Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "MNV_artifact"
+      "lbl" : "N4_methylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002177",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001292",
       "meta" : {
         "definition" : {
-          "val" : "A duplication that is the result of base-calling or assembly error.",
-          "xrefs" : [ ]
+          "val" : "5-hydroxymethylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:084"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "duplication artifact",
+          "val" : "hm5C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5-hydroxymethylcytidine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five hydroxymethylcytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T15:26:00Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "duplication_artifact"
+      "lbl" : "five_hydroxymethylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002178",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001291",
       "meta" : {
         "definition" : {
-          "val" : "An SNV that is the result of base-calling or assembly error.",
-          "xrefs" : [ ]
+          "val" : "N4,2'-O-dimethylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:083"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SNV artifact",
+          "val" : "N4 2 prime O dimethylcytidine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N4,2'-O-dimethylcytidine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m4Cm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T15:26:49Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SNV_artifact"
+      "lbl" : "N4_2_prime_O_dimethylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002175",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002139",
       "meta" : {
         "definition" : {
-          "val" : "An insertion that is the result of base-calling or assembly error.",
-          "xrefs" : [ ]
+          "val" : "This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insertion artifact",
+          "val" : "TEC",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "to_be_experimentally_confirmed_transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -35114,127 +39303,133 @@
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T15:17:42Z"
+          "val" : "2016-08-23T16:28:07Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insertion_artifact"
+      "lbl" : "unconfirmed_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002176",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002137",
       "meta" : {
         "definition" : {
-          "val" : "A substitution that is the result of base-calling or assembly error.",
-          "xrefs" : [ ]
+          "val" : "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "substitution artifact",
+          "val" : "T_cell_receptor_V_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T15:18:12Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:21:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "substitution_artifact"
+      "lbl" : "TR_V_Gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002173",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002138",
       "meta" : {
         "definition" : {
-          "val" : "An indel that is the result of base-calling or assembly error.",
-          "xrefs" : [ ]
+          "val" : "A transcript feature that has been predicted but is not yet validated.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "indel artifact",
+          "val" : "predicted transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:27:38Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T15:16:20Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "indel_artifact"
+      "lbl" : "predicted_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002174",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002135",
       "meta" : {
         "definition" : {
-          "val" : "A deletion that is the result of base-calling or assembly error.",
-          "xrefs" : [ ]
+          "val" : "A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "deletion artifact",
+          "val" : "T_cell_receptor_D_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T15:17:11Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2016-08-23T16:20:06Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "deletion_artifact"
+      "lbl" : "TR_D_Gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002171",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001287",
       "meta" : {
         "definition" : {
-          "val" : "A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus.",
-          "xrefs" : [ "PMID:10338204", "PMID:15071557", "PMID:24012755" ]
+          "val" : "5,2'-O-dimethylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:026"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "telomeric D loop",
+          "val" : "5,2'-O-dimethylcytidine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five two prime O dimethylcytidine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m5Cm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This definition is from GO:0061820 telomeric D-loop disassembly."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-01T13:12:11Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "telomeric_D_loop"
+      "lbl" : "five_two_prime_O_dimethylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002172",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002136",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process.",
-          "xrefs" : [ ]
+          "val" : "A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence alteration artifact",
+          "val" : "T_cell_receptor_J_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -35245,416 +39440,399 @@
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-08-18T13:43:26Z"
+          "val" : "2016-08-23T16:20:36Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_alteration_artifact"
+      "lbl" : "TR_J_Gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002170",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001286",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron).",
-          "xrefs" : [ ]
+          "val" : "5-formylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:025"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice donor region variant",
+          "val" : "f5C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five formylcytidine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5-formylcytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2017-07-31T13:48:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_donor_region_variant"
+      "lbl" : "five_formylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002199",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002133",
       "meta" : {
         "definition" : {
-          "val" : "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.",
+          "val" : "A T-cell receptor germline gene.",
           "xrefs" : [ ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:unitary",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "unitary pseudogenic tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:tRNA",
+          "val" : "TR_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T12:16:59Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:17:12Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unitary_pseudogenic_tRNA"
+      "lbl" : "T_cell_receptor_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002197",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001289",
       "meta" : {
         "definition" : {
-          "val" : "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.",
-          "xrefs" : [ ]
+          "val" : "Lysidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "processed pseudogenic tRNA",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Lysidine"
         }, {
+          "val" : "RNAMOD:028"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:processed",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:tRNA",
-          "xrefs" : [ ]
+          "val" : "k2C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T12:10:10Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "processed_pseudogenic_tRNA"
+      "lbl" : "lysidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002198",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002134",
       "meta" : {
         "definition" : {
-          "val" : "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.",
-          "xrefs" : [ ]
+          "val" : "A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unprocessed pseudogenic tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:unprocessed",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:tRNA",
+          "val" : "T_cell_receptor_C_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T12:14:34Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2016-08-23T16:19:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unprocessed_pseudogenic_tRNA"
+      "lbl" : "TR_C_Gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002195",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001288",
       "meta" : {
         "definition" : {
-          "val" : "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.",
-          "xrefs" : [ ]
+          "val" : "N4-acetyl-2'-O-methylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:027"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unitary pseudogenic rRNA",
+          "val" : "N4-acetyl-2'-O-methylcytidine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:rRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "N4 acetyl 2 prime O methylcytidine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:unitary",
-          "xrefs" : [ ]
+          "val" : "ac4Cm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T11:51:59Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unitary_pseudogenic_rRNA"
+      "lbl" : "N4_acetyl_2_prime_O_methylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002196",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002131",
       "meta" : {
         "definition" : {
-          "val" : "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.",
-          "xrefs" : [ ]
+          "val" : "A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence.",
+          "xrefs" : [ "GENECODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "allelic pseudogenic rRNA",
+          "val" : "sense_intronic_non-coding_RNA",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:rRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "sense_intronic_lncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:allelic",
+          "val" : "sense intronic lncRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sense_intronic",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T11:53:13Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001903"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:15:02Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "allelic_pseudogenic_rRNA"
+      "lbl" : "sense_intronic_lncRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002193",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001283",
       "meta" : {
         "definition" : {
-          "val" : "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.",
-          "xrefs" : [ ]
+          "val" : "2'-O-methylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:022"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "processed pseudogenic rRNA",
+          "val" : "two prime O methylcytidine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:rRNA",
-          "xrefs" : [ ]
+          "pred" : "hasExactSynonym",
+          "val" : "Cm",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:processed",
+          "val" : "2'-O-methylcytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T11:43:58Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "processed_pseudogenic_rRNA"
+      "lbl" : "two_prime_O_methylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002194",
+      "id" : "http://purl.obolibrary.org/obo/so#VAR",
+      "lbl" : "variant annotation term"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001282",
       "meta" : {
         "definition" : {
-          "val" : "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.",
-          "xrefs" : [ ]
+          "val" : "5-methylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:021"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:unprocessed",
+          "val" : "five methylcytidine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "unprocessed pseudogenic rRNA",
-          "xrefs" : [ ]
+          "val" : "m5C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:rRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "5-methylcytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-08T11:49:41Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unprocessed_pseudogenic_rRNA"
+      "lbl" : "five_methylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002191",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002132",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs.",
-          "xrefs" : [ ]
+          "val" : "A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence.",
+          "xrefs" : [ "GENECODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579." ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "pred" : "hasExactSynonym",
+          "val" : "sense_overlap_lncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:imprinting_control_region",
+          "val" : "sense overlap lncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "imprinting control region",
+          "val" : "sense_overlapping",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-04T17:35:34Z"
+          "val" : "2016-08-23T16:16:13Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "imprinting_control_region"
+      "lbl" : "sense_overlap_lncRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002192",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001285",
       "meta" : {
         "definition" : {
-          "val" : "A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites).",
-          "xrefs" : [ ]
+          "val" : "N4-acetylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:024"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:flanking",
+          "val" : "N4 acetylcytidine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "pred" : "hasExactSynonym",
+          "val" : "N4-acetylcytidine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "flanking repeat",
-          "xrefs" : [ ]
+          "val" : "ac4C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-05T16:27:21Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "flanking_repeat"
+      "lbl" : "N4_acetylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002190",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001284",
       "meta" : {
         "definition" : {
-          "val" : "A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator.",
-          "xrefs" : [ "NCBI:cf" ]
+          "val" : "2-thiocytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:023"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:enhancer_blocking_element",
+          "val" : "two thiocytidine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "enhancer blocking element",
+          "val" : "2-thiocytidine",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "insulator",
-          "xrefs" : [ ]
+          "pred" : "hasExactSynonym",
+          "val" : "s2C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf)."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2018-01-04T17:28:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "enhancer_blocking_element"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#SOFA",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "SO feature annotation"
-        } ]
-      },
-      "type" : "PROPERTY"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#ebi_variants",
-      "type" : "PROPERTY",
-      "lbl" : "ensembl variant terms"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
-      "type" : "PROPERTY",
-      "lbl" : "database_cross_reference"
+      "lbl" : "two_thiocytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#recombined_from",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002130",
       "meta" : {
+        "definition" : {
+          "val" : "A transcript that contains a CDS but has no stop codon before the polyA site is reached.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "non_stop_decay_transcript",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T02:21:03Z"
+          "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:11:34Z"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "recombined_from"
+      "type" : "CLASS",
+      "lbl" : "NSD_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000819",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001281",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome originating in a mitochondria.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "3-methylcytidine is a modified cytidine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:020"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mitochondrial chromosome",
+          "val" : "m3C",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3-methylcytidine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "three methylcytidine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -35663,18 +39841,30 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mitochondrial_chromosome"
+      "lbl" : "three_methylcytidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000818",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001280",
       "meta" : {
         "definition" : {
-          "val" : "A gene that rescues.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "2'-O-methylinosine is a modified inosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
+        "xrefs" : [ {
+          "val" : "RNAMOD:081"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "wild type rescue gene",
+          "val" : "2'-O-methylinosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "two prime O methylinosine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Im",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -35682,55 +39872,96 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "wild_type_rescue_gene"
+      "lbl" : "two_prime_O_methylinosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000815",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002128",
       "meta" : {
         "definition" : {
-          "val" : "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.",
-          "xrefs" : [ "PMID:15992143" ]
+          "val" : "Mitochondrial rRNA is an RNA component of the small or large subunits of mitochondrial ribosomes.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "Updated definition to be consistent with format of other rRNA definitions on 10 June 2021. Requested by EBI. See GitHub Issue #493." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mini gene",
+          "val" : "mitochondrial_rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mt rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mitochondrial rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Mt_rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:08:59Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mini_gene"
+      "lbl" : "mt_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000814",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002129",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Mitochondrial transfer RNA.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Mt_tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mitochondrial_tRNA",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:10:17Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rescue"
+      "lbl" : "mt_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000817",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001279",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "1,2'-O-dimethylinosine is a modified inosine.",
+          "xrefs" : [ "http://library.med.utah.edu/RNAmods/" ]
         },
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Wild_type"
-        }, {
-          "val" : "loinc:LA9658-1"
+          "val" : "RNAMOD:019"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "wild type",
+          "val" : "m'Im",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "1,2'-O-dimethylinosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "one two prime O dimethylinosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -35739,513 +39970,683 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "wild_type"
+      "lbl" : "one_two_prime_O_dimethylinosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000816",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002126",
       "meta" : {
         "definition" : {
-          "val" : "A gene that rescues.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html", "IGMT:http://www.imgt.org/IMGTScientificChart/SequenceDescription/Keywords.php" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rescue gene",
+          "val" : "IGV_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "IG_variable_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Immunoglobulin_variable_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:02:09Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rescue_gene"
+      "lbl" : "IG_V_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000811",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002127",
       "meta" : {
         "definition" : {
-          "val" : "A cDNA clone invalidated by genomic contamination.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A gene that encodes a long non-coding RNA.",
+          "xrefs" : [ "GENCODE:http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "genomically contaminated cDNA clone",
+          "val" : "lnc_RNA_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "long_non_coding_RNA_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "lnc RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-08-23T16:03:33Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "genomically_contaminated_cDNA_clone"
+      "lbl" : "lncRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000810",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002168",
       "meta" : {
         "definition" : {
-          "val" : "A cDNA clone invalidated because it is chimeric.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression.",
+          "xrefs" : [ "PMID:22421878" ]
         },
+        "xrefs" : [ {
+          "val" : "https://en.wikipedia.org/wiki/RNA_thermometer"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chimeric cDNA clone",
+          "val" : "RNA thermometer",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RNA thermoregulator",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RNAT",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "thermoregulator",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-07-17T10:07:45Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chimeric_cDNA_clone"
+      "lbl" : "RNA_thermometer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000813",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002169",
       "meta" : {
         "definition" : {
-          "val" : "A cDNA invalidated clone by partial processing.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "partially processed cDNA clone",
+          "val" : "splice polypyrimidine tract variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-07-31T13:40:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "partially_processed_cDNA_clone"
+      "lbl" : "splice_polypyrimidine_tract_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000812",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002166",
       "meta" : {
         "definition" : {
-          "val" : "A cDNA clone invalidated by polyA priming.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A ref_miRNA (RefSeq-miRNA) sequence is assigned at the creation of a new mature miRNA entry in a database. The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA.",
+          "xrefs" : [ "PMID:26453491" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polyA primed cDNA clone",
+          "val" : "RefSeq-miRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RefSeq miRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ref miRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-06-22T11:05:49Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polyA_primed_cDNA_clone"
+      "lbl" : "ref_miRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000808",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002167",
       "meta" : {
         "definition" : {
-          "val" : "A cDNA clone that has been validated.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA.",
+          "xrefs" : [ "PMID:26453491" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "validated cDNA clone",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-06-22T11:09:42Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "validated_cDNA_clone"
+      "lbl" : "isomiR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000807",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002164",
       "meta" : {
         "definition" : {
-          "val" : "A tag that is engineered.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated.",
+          "xrefs" : [ "PMID:18552846", "http://www.actrec.gov.in/histome/ptm_sp.php?ptm_sp=H2BK5ac" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered tag",
+          "val" : "H2BK5ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2BK5 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-05-17T15:22:58Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_tag"
+      "lbl" : "H2BK5_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000809",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002165",
       "meta" : {
         "definition" : {
-          "val" : "A cDNA clone that is invalid.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "invalidated cDNA clone",
+          "val" : "trinucleotide repeat expansion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-06-02T10:43:42Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "invalidated_cDNA_clone"
+      "lbl" : "trinucleotide_repeat_expansion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000804",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002162",
       "meta" : {
         "definition" : {
-          "val" : "A region that is engineered.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A short tandem repeat variant containing more repeat units than the reference sequence.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "engineered sequence",
+          "val" : "short tandem repeat expansion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "construct",
+          "val" : "str expansion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-04-26T12:51:26Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_region"
+      "lbl" : "short_tandem_repeat_expansion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000803",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002163",
       "meta" : {
         "definition" : {
-          "val" : "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.",
-          "xrefs" : [ "FB:gm" ]
+          "val" : "A short tandem repeat variant containing fewer repeat units than the reference sequence.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "assortment derived aneuploid",
+          "val" : "short tandem repeat contraction",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "str contraction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-04-26T12:52:33Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "assortment_derived_aneuploid"
+      "lbl" : "short_tandem_repeat_contraction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000806",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002160",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that changes the length of one or more sequence features.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence length variant",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-04-26T12:31:12Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "fusion"
+      "lbl" : "sequence_length_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000805",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002161",
       "meta" : {
         "definition" : {
-          "val" : "A region that is engineered and foreign.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered foreign region",
+          "val" : "str change",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "short tandem repeat change",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-04-26T12:50:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_foreign_region"
+      "lbl" : "short_tandem_repeat_change"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000800",
+      "id" : "http://purl.obolibrary.org/obo/so#part_of",
       "meta" : {
         "definition" : {
-          "val" : "A multi-chromosome duplication aberration generated by reassortment of other aberration components.",
-          "xrefs" : [ "FB:gm" ]
+          "val" : "X part_of Y if X is a subregion of Y.",
+          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "assortment derived duplication",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Example: amino_acid part_of polypeptide." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "assortment_derived_duplication"
+      "type" : "PROPERTY",
+      "lbl" : "part_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000802",
+      "id" : "http://purl.obolibrary.org/obo/so#member_of",
       "meta" : {
-        "definition" : {
-          "val" : "A multi-chromosome deficiency aberration generated by reassortment of other aberration components.",
-          "xrefs" : [ "FB:gm" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "assortment-derived deficiency",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "assortment_derived_deficiency"
+      "type" : "PROPERTY",
+      "lbl" : "member_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000801",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002159",
       "meta" : {
         "definition" : {
-          "val" : "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.",
-          "xrefs" : [ "FB:gm" ]
+          "val" : "A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence FXGKGX[RK]LG.",
+          "xrefs" : [ "PMID:17083136", "PMID:27655872" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "assortment derived deficiency plus duplication",
+          "val" : "SHP box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-12-15T09:48:38Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "assortment_derived_deficiency_plus_duplication"
+      "lbl" : "SHP_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000136",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002157",
       "meta" : {
         "definition" : {
-          "val" : "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome.",
-          "xrefs" : [ "PMID:6804304" ]
+          "val" : "A gene cassette array containing H+ mating type specific information.",
+          "xrefs" : [ "PMID:18354497" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "autosynaptic chromosome",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)A",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-11-17T10:59:00Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "autosynaptic_chromosome"
+      "lbl" : "Mat2P"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000134",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002158",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing polypeptide fusion",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing polypeptide fusion",
-          "xrefs" : [ ]
-        } ],
+        "definition" : {
+          "val" : "A gene cassette array containing H- mating type specific information.",
+          "xrefs" : [ "PMID:18354497" ]
+        },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001616"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-11-17T11:02:27Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_polypeptide_fusion"
+      "lbl" : "Mat3M"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000138",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002155",
       "meta" : {
         "definition" : {
-          "val" : "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase.",
+          "xrefs" : [ "NCBI:cf", "SO:ke" ]
         },
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_recomb",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "homo compound chromosome",
+          "val" : "INSDC_qualifier:meiotic_recombination",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "homo-compound chromosome",
+          "val" : "meiotic recombination region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:meiotic",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-28T10:34:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "homo_compound_chromosome"
+      "lbl" : "meiotic_recombination_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000719",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002156",
       "meta" : {
         "definition" : {
-          "val" : "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.",
-          "xrefs" : [ "FB:WG" ]
+          "val" : "A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'.",
+          "xrefs" : [ "PMID:1748287", "PMID:7623803" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Requested by Antonia Lock" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pseudochromosome",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "superscaffold",
+          "val" : "CArG box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-28T10:42:06Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ultracontig"
+      "lbl" : "CArG_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000716",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002153",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA that has the quality dicistronic.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms.",
+          "xrefs" : [ "NCBI:dm", "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "dicistronic mRNA",
+          "val" : "genic 5 prime transcript variant",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "dicistronic processed transcript",
+          "pred" : "hasExactSynonym",
+          "val" : "genic 5' transcript variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "genic upstream transcript variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-28T10:23:17Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dicistronic_mRNA"
+      "lbl" : "genic_upstream_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000715",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002154",
       "meta" : {
         "definition" : {
-          "val" : "A motif that is active in RNA sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells.",
+          "xrefs" : [ "NCBI:cf", "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_recomb",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "RNA motif",
+          "val" : "INSDC_qualifier:mitotic_recombination",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:mitotic",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mitotic recombination region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-28T10:33:54Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_motif"
+      "lbl" : "mitotic_recombination_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000718",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002151",
       "meta" : {
         "definition" : {
-          "val" : "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons.",
-          "xrefs" : [ "SGD:rb" ]
+          "val" : "A uORF beginning with a codon other than AUG.",
+          "xrefs" : [ "PMID:26684391", "PMID:27313038" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "blocked reading frame",
+          "val" : "non AUG initiated uORF",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-26T09:37:45Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term requested by Rama from SGD."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "blocked_reading_frame"
+      "lbl" : "non_AUG_initiated_uORF"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000717",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002152",
       "meta" : {
         "definition" : {
-          "val" : "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.",
-          "xrefs" : [ "SGD:rb" ]
+          "val" : "A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms.",
+          "xrefs" : [ "NCBI:dm", "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Reading_frame"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "reading frame",
+          "val" : "genic 3' transcript variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "genic downstream transcript variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "genic 3 prime transcript variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-28T10:20:55Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reading_frame"
+      "lbl" : "genic_downstream_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000712",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002150",
       "meta" : {
         "definition" : {
-          "val" : "A gene encoding a transcript that has a translational frameshift.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A uORF beginning with the canonical start codon AUG.",
+          "xrefs" : [ "PMID:26684391", "PMID:27313038" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with transcript with translational frameshift",
+          "val" : "AUG initiated uORF",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-26T09:37:11Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_transcript_with_translational_frameshift"
+      "lbl" : "AUG_initiated_uORF"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000140",
+      "id" : "http://purl.obolibrary.org/obo/SO_2000061",
       "meta" : {
         "definition" : {
-          "val" : "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them.",
-          "xrefs" : [ "FB:reference_manual", "SO:ke" ]
+          "val" : "The sequence referred to by an entry in a databank such as GenBank or SwissProt.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "hetero compound chromosome",
+          "val" : "databank entry",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "hetero-compound chromosome",
+          "pred" : "hasRelatedSynonym",
+          "val" : "accession",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -36254,826 +40655,1042 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "hetero_compound_chromosome"
+      "lbl" : "databank_entry"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000711",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002148",
       "meta" : {
         "definition" : {
-          "val" : "A gene with mRNA recoded by translational bypass.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
+          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with mRNA recoded by translational bypass",
+          "val" : "H2AZK13ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2AZK13 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2A.ZK13ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-25T14:23:50Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_mRNA_recoded_by_translational_bypass"
+      "lbl" : "H2AZK13_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000714",
+      "id" : "http://purl.obolibrary.org/obo/so#translation_of",
       "meta" : {
         "definition" : {
-          "val" : "A region of nucleotide sequence corresponding to a known motif.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "X is translation of Y if Y is translated by ribosome to create X.",
+          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "nucleotide motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_feature",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:nucleotide_motif",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Example: Polypeptide translation_of CDS." ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-08-19T12:09:59Z"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "nucleotide_motif"
+      "type" : "PROPERTY",
+      "lbl" : "translation_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000713",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002149",
       "meta" : {
         "definition" : {
-          "val" : "A motif that is active in the DNA form of the sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated.",
+          "xrefs" : [ "PMID:19385636", "PMID:24316985", "PMID:27087541" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/DNA_motif"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DNA motif",
+          "val" : "H2AZK15 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2AZK15ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2A.ZK15ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-10-25T14:24:08Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DNA_motif"
+      "lbl" : "H2AZK15_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000144",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002188",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product.",
+          "xrefs" : [ "Clingen:mb" ]
         },
+        "comments" : [ "A functional_gene_region is a sequence feature that resides within a gene. But it is typically the corresponding region of translated/transcribed sequence in a gene product, that performs the molecular function qualifying it as a functional_gene_region. Here, a functional_gene_region must contribute directly to the molecular function of the gene product - regions that code for purely structural elements in a gene product that connect such directly functional elements together are not considered functional_gene_regions. Examples of regions considered 'functional' include those encoding enzymatic activity, binding activity, regions required for localization or membrane association, channel-forming regions, and signal peptides or other elements critical for processing of a gene product. In addition, regions that function at the genomic/DNA level are also included - e.g. regions of sequence known to be critical for binding transcription or splicing factors." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "free duplication",
+          "val" : "functional gene region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-12-15T11:08:43Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "free_duplication"
+      "lbl" : "functional_gene_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000143",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002189",
       "meta" : {
         "definition" : {
-          "val" : "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres.",
-          "xrefs" : [ "FB:manual" ]
+          "val" : "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:gene",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "laevosynaptic chromosome",
+          "val" : "INSDC_qualifier:allelic",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "allelic pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-03T15:47:32Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "laevosynaptic_chromosome"
+      "lbl" : "allelic_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000142",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002186",
       "meta" : {
         "definition" : {
-          "val" : "An autosynaptic chromosome carrying the two right (D = dextro) telomeres.",
-          "xrefs" : [ "FB:manual" ]
+          "val" : "A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "dexstrosynaptic chromosome",
+          "val" : "mutational hotspot",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-11-07T12:27:51Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dexstrosynaptic_chromosome"
+      "lbl" : "mutational_hotspot"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000710",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002187",
       "meta" : {
         "definition" : {
-          "val" : "A gene encoding an mRNA that has the stop codon redefined as selenocysteine.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An insertion of sequence from the HERV family of mobile elements with respect to a reference.",
+          "xrefs" : [ "NCBI:th" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with stop codon redefined as selenocysteine",
+          "val" : "HERV insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-11-20T11:52:51Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_stop_codon_redefined_as_selenocysteine"
+      "lbl" : "HERV_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000141",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002184",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome that occurred by the division of a larger chromosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that encodes a sense intronic long non-coding RNA.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromosome fission",
+          "val" : "sense intronic lncRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sense_intronic_lncRNA_gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sense intronic ncRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-09-27T11:03:50Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosome_fission"
+      "lbl" : "sense_intronic_lncRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000126",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002185",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand.",
+          "xrefs" : [ "https://www.gencodegenes.org/pages/biotypes.html" ]
         },
+        "comments" : [ "This is a gencode term. See GitHub Issue #408. Synonyms \"bidirectional promoter lncRNA gene\" and \"bidirectional_promoter_lncRNA_gene\" added 23 April 2021 by David Sant. See GitHub Issue #506." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting transcript secondary structure",
+          "pred" : "hasExactSynonym",
+          "val" : "bidirectional promoter lncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting transcript secondary structure",
+          "val" : "bidirectional promoter lncRNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "bidirectional_promoter_lncRNA_gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001596"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-10-03T11:43:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_transcript_secondary_structure"
+      "lbl" : "bidirectional_promoter_lncRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000125",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002182",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing gain of function of polypeptide",
+        "definition" : {
+          "val" : "A gene that encodes an antisense long, non-coding RNA.",
           "xrefs" : [ ]
-        }, {
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gain of function of polypeptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing gain of function of polypeptide",
+          "val" : "antisense lncRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001557"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-09-27T10:44:00Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_gain_of_function_of_polypeptide"
+      "lbl" : "antisense_lncRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000124",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002183",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that encodes a sense overlap long non-coding RNA.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Updating the names of sense_intronic_ncRNA (SO:0002131), sense_overlap_ncRNA (SO:0002132), sense_overlap_ncRNA_gene (SO:0002183), and sense_intronic_ncRNA_gene (SO:0002184) to _lncRNA. See GitHub Issue #579." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing partial loss of function of polypeptide",
+          "pred" : "hasExactSynonym",
+          "val" : "sense_overlap_lncRNA_gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "partial loss of function of polypeptide",
+          "val" : "sense overlap lncRNA gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing partial loss of function of polypeptide",
+          "val" : "sense overlap ncRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001561"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-09-27T10:48:05Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_partial_loss_of_function_of_polypeptide"
+      "lbl" : "sense_overlap_lncRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000123",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002180",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that encodes an enzymatic RNA.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "polypeptide_post-translational_processing_affected",
+          "pred" : "hasExactSynonym",
+          "val" : "enzymatic RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-09-27T10:30:27Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_post_translational_processing_affected"
+      "lbl" : "enzymatic_RNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000127",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002181",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that encodes a ribozyme.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing compensatory transcript secondary structure mutation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing compensatory transcript secondary structure mutation",
+          "val" : "ribozyme gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001597"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-09-27T10:31:09Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_compensatory_transcript_secondary_structure_mutation"
+      "lbl" : "ribozyme_gene"
     }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#consider",
+      "id" : "http://purl.obolibrary.org/obo/IAO_0000115",
       "type" : "PROPERTY",
-      "lbl" : "consider"
+      "lbl" : "definition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000709",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002179",
       "meta" : {
         "definition" : {
-          "val" : "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "An MNV that is the result of base-calling or assembly error.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL2 acceptor site",
+          "val" : "MNV artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T15:27:21Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL2_acceptor_site"
+      "lbl" : "MNV_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000708",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002177",
       "meta" : {
         "definition" : {
-          "val" : "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.",
-          "xrefs" : [ "SO:nlw" ]
+          "val" : "A duplication that is the result of base-calling or assembly error.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SL1 acceptor site",
+          "val" : "duplication artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T15:26:00Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SL1_acceptor_site"
+      "lbl" : "duplication_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000705",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002178",
       "meta" : {
         "definition" : {
-          "val" : "Two or more adjacent copies of a region (of length greater than 1).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An SNV that is the result of base-calling or assembly error.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://www.sci.sdsu.edu/~smaloy/Glossary/T.html"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Tandem_repeat"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:tandem",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "tandem repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "val" : "SNV artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T15:26:49Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tandem_repeat"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#adjacent_to",
-      "meta" : {
-        "definition" : {
-          "val" : "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.",
-          "xrefs" : [ "PMID:20226267", "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "adjacent_to"
+      "lbl" : "SNV_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000704",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002175",
       "meta" : {
         "definition" : {
-          "val" : "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.",
-          "xrefs" : [ "SO:immuno_workshop" ]
+          "val" : "An insertion that is the result of base-calling or assembly error.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Gene"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:gene",
+          "val" : "insertion artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T15:17:42Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene"
+      "lbl" : "insertion_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000707",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002176",
       "meta" : {
         "definition" : {
-          "val" : "The 5' five prime splice site region of the donor RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A substitution that is the result of base-calling or assembly error.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "trans splice donor site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "trans-splice donor site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "5 prime trans splice site",
+          "val" : "substitution artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T15:18:12Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "SL RNA contains a donor site."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trans_splice_donor_site"
+      "lbl" : "substitution_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000706",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002173",
       "meta" : {
         "definition" : {
-          "val" : "The 3' splice site of the acceptor primary transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An indel that is the result of base-calling or assembly error.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "trans splice acceptor site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "3' trans splice site",
+          "val" : "indel artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T15:16:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trans_splice_acceptor_site"
+      "lbl" : "indel_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000701",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002174",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence where the validity of the base calling is questionable.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A deletion that is the result of base-calling or assembly error.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "possible base call error",
+          "val" : "deletion artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T15:17:11Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "possible_base_call_error"
+      "lbl" : "deletion_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000700",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002171",
       "meta" : {
         "definition" : {
-          "val" : "A comment about the sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus.",
+          "xrefs" : [ "PMID:10338204", "PMID:15071557", "PMID:24012755" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "This definition is from GO:0061820 telomeric D-loop disassembly." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "telomeric D loop",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-01T13:12:11Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "remark"
+      "lbl" : "telomeric_D_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000703",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002172",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence implicated in an experimental result.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "experimental result region",
+          "val" : "sequence alteration artifact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-08-18T13:43:26Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "experimental_result_region"
+      "lbl" : "sequence_alteration_artifact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000702",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002170",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence where there may have been an error in the assembly.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron).",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "possible assembly error",
+          "val" : "splice donor region variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2017-07-31T13:48:32Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "possible_assembly_error"
+      "lbl" : "splice_donor_region_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000132",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002199",
       "meta" : {
         "definition" : {
-          "val" : "The effect of a change in nucleotide sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence variant effect",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:unitary",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "unitary pseudogenic tRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.\nUpdated after discussion with Peter Taschner - Feb 09."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T12:16:59Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_effect"
+      "lbl" : "unitary_pseudogenic_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000159",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002197",
       "meta" : {
         "definition" : {
-          "val" : "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)eTp",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:tRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "uninverted intrachromosomal transposition",
+          "val" : "INSDC_qualifier:processed",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "processed pseudogenic tRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T12:10:10Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "uninverted_intrachromosomal_transposition"
+      "lbl" : "processed_pseudogenic_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000158",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002198",
       "meta" : {
         "definition" : {
-          "val" : "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inverted intrachromosomal transposition",
+          "val" : "INSDC_qualifier:unprocessed",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)iTp",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "unprocessed pseudogenic tRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T12:14:34Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inverted_intrachromosomal_transposition"
+      "lbl" : "unprocessed_pseudogenic_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000157",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002195",
       "meta" : {
         "definition" : {
-          "val" : "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "uninverted interchromosomal transposition",
+          "val" : "INSDC_qualifier:unitary",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)eTp",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "unitary pseudogenic rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T11:51:59Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "uninverted_interchromosomal_transposition"
+      "lbl" : "unitary_pseudogenic_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000156",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002196",
       "meta" : {
         "definition" : {
-          "val" : "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)iTp",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:allelic",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:rRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "inverted interchromosomal transposition",
+          "val" : "allelic pseudogenic rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T11:53:13Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inverted_interchromosomal_transposition"
+      "lbl" : "allelic_pseudogenic_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#trans_spliced_from",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002193",
       "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T02:22:14Z"
+        "definition" : {
+          "val" : "The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:processed",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:rRNA",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "processed pseudogenic rRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "nicole"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T11:43:58Z"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "trans_spliced_from"
+      "type" : "CLASS",
+      "lbl" : "processed_pseudogenic_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000738",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002194",
       "meta" : {
+        "definition" : {
+          "val" : "The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nuclear sequence",
+          "val" : "unprocessed pseudogenic rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:unprocessed",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-08T11:49:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclear_sequence"
+      "lbl" : "unprocessed_pseudogenic_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000737",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002191",
       "meta" : {
+        "definition" : {
+          "val" : "A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Moved from is_a regulatory_region (SO:0005836) to is_a epigenetically_modified_region (SO:0001720) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530." ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "mitochondrial sequence",
+          "val" : "INSDC_qualifier:imprinting_control_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "imprinting control region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-04T17:35:34Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mitochondrial_sequence"
+      "lbl" : "imprinting_control_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000739",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002192",
       "meta" : {
+        "definition" : {
+          "val" : "A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites).",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "nucleomorphic sequence",
+          "val" : "flanking repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:flanking",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-05T16:27:21Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nucleomorphic_sequence"
+      "lbl" : "flanking_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000162",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002190",
       "meta" : {
         "definition" : {
-          "val" : "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator.",
+          "xrefs" : [ "NCBI:cf" ]
         },
+        "comments" : [ "Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unorientated intrachromosomal transposition",
+          "val" : "enhancer blocking element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:enhancer_blocking_element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)uTp",
+          "val" : "insulator",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "FLAG - definition describes an unknown."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2018-01-04T17:28:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unoriented_intrachromosomal_transposition"
+      "lbl" : "enhancer_blocking_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000734",
+      "id" : "http://purl.obolibrary.org/obo/so#ebi_variants",
+      "lbl" : "ensembl variant terms"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
+      "type" : "PROPERTY",
+      "lbl" : "database_cross_reference"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#recombined_from",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-08-19T02:21:03Z"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "recombined_from"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000819",
       "meta" : {
         "definition" : {
-          "val" : "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.",
-          "xrefs" : [ "http://mged.sourceforge.net/ontologies/MGEDontology.php" ]
+          "val" : "A chromosome originating in a mitochondria.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "exemplar mRNA",
+          "val" : "mitochondrial chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added for the MO people."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exemplar_mRNA"
+      "lbl" : "mitochondrial_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000161",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000818",
       "meta" : {
         "definition" : {
-          "val" : "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A gene that rescues.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)uTp",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "unorientated interchromosomal transposition",
+          "val" : "wild type rescue gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "FLAG - term describes an unknown."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unoriented_interchromosomal_transposition"
+      "lbl" : "wild_type_rescue_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000733",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000815",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a located_sequence_feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA.",
+          "xrefs" : [ "PMID:15992143" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "feature attribute",
+          "val" : "mini gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37082,54 +41699,55 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "feature_attribute"
+      "lbl" : "mini_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000736",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000814",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "organelle sequence",
-          "xrefs" : [ ]
-        } ],
+        "definition" : {
+          "val" : "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "organelle_sequence"
+      "lbl" : "rescue"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000160",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000817",
       "meta" : {
         "definition" : {
-          "val" : "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)uDp",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "loinc:LA9658-1"
         }, {
+          "val" : "http://en.wikipedia.org/wiki/Wild_type"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unoriented insertional duplication",
+          "val" : "wild type",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Flag - unknown in the definition."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unoriented_insertional_duplication"
+      "lbl" : "wild_type"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000735",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000816",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that rescues.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence location",
+          "val" : "rescue gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37138,22 +41756,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_location"
+      "lbl" : "rescue_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000730",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000811",
       "meta" : {
         "definition" : {
-          "val" : "A gap in the sequence of known length. The unknown bases are filled in with N's.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A cDNA clone invalidated by genomic contamination.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasNarrowSynonym",
-          "val" : "INSDC_feature:assembly_gap",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:gap",
+          "val" : "genomically contaminated cDNA clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37162,16 +41775,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gap"
+      "lbl" : "genomically_contaminated_cDNA_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000732",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000810",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an unverified region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A cDNA clone invalidated because it is chimeric.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Predicted"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "chimeric cDNA clone",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -37179,47 +41794,36 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "predicted"
+      "lbl" : "chimeric_cDNA_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000731",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000813",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a feature that is incomplete.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A cDNA invalidated clone by partial processing.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "fragment",
+          "val" : "partially processed cDNA clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term added because of request by MO people."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "fragmentary"
+      "lbl" : "partially_processed_cDNA_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000148",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000812",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A cDNA clone invalidated by polyA priming.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inversion cum translocation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)T",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)InT",
+          "val" : "polyA primed cDNA clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37228,25 +41832,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inversion_cum_translocation"
+      "lbl" : "polyA_primed_cDNA_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000147",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000808",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A cDNA clone that has been validated.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "deficient translocation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)Df",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)DfT",
+          "val" : "validated cDNA clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37255,21 +41851,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "deficient_translocation"
+      "lbl" : "validated_cDNA_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000145",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000807",
       "meta" : {
         "definition" : {
-          "val" : "A ring chromosome which is a copy of another chromosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A tag that is engineered.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)R",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "free ring duplication",
+          "val" : "engineered tag",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37278,21 +41870,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "free_ring_duplication"
+      "lbl" : "engineered_tag"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000149",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000809",
       "meta" : {
         "definition" : {
-          "val" : "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A cDNA clone that is invalid.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bipartite duplication",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)bDp",
+          "val" : "invalidated cDNA clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37301,121 +41889,96 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bipartite_duplication"
+      "lbl" : "invalidated_cDNA_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000727",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000804",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network.",
-          "xrefs" : [ "PMID:19660565", "SO:SG" ]
+          "val" : "A region that is engineered.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TF module",
+          "val" : "engineered region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "cis regulatory module",
+          "val" : "construct",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "transcription factor module",
+          "val" : "engineered sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Stephen Grossmann Dec 2004."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CRM"
+      "lbl" : "engineered_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000726",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000803",
       "meta" : {
         "definition" : {
-          "val" : "The simplest repeated component of a repeat region. A single repeat.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication.",
+          "xrefs" : [ "FB:gm" ]
         },
-        "xrefs" : [ {
-          "val" : "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "repeat unit",
+          "val" : "assortment derived aneuploid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added to comply with the feature table. A single repeat."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "repeat_unit"
+      "lbl" : "assortment_derived_aneuploid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000729",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000806",
       "meta" : {
         "definition" : {
-          "val" : "An attribute of protein-coding genes where the initial protein product contains an intein.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "intein containing",
+          "val" : "When two regions of DNA are joined together that are not normally together.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intein_containing"
+      "lbl" : "fusion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000728",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000805",
       "meta" : {
         "definition" : {
-          "val" : "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that is engineered and foreign.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Intein"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "protein intron",
+          "pred" : "hasExactSynonym",
+          "val" : "engineered foreign region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Intein-mediated protein splicing occurs after mRNA has been translated into a protein."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intein"
+      "lbl" : "engineered_foreign_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000723",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000800",
       "meta" : {
         "definition" : {
-          "val" : "Genomic sequence removed from the genome, as a normal event, by a process of recombination.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A multi-chromosome duplication aberration generated by reassortment of other aberration components.",
+          "xrefs" : [ "FB:gm" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:iDNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "intervening DNA",
+          "val" : "assortment derived duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37424,21 +41987,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "iDNA"
+      "lbl" : "assortment_derived_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000151",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000802",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A multi-chromosome deficiency aberration generated by reassortment of other aberration components.",
+          "xrefs" : [ "FB:gm" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)bIn",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "bipartite inversion",
+          "val" : "assortment-derived deficiency",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37447,43 +42006,40 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bipartite_inversion"
+      "lbl" : "assortment_derived_deficiency"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000722",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000801",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a polycistronic mRNA.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication.",
+          "xrefs" : [ "FB:gm" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with dicistronic processed transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "gene with dicistronic mRNA",
+          "val" : "assortment derived deficiency plus duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by MA nov 19 2004."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_dicistronic_mRNA"
+      "lbl" : "assortment_derived_deficiency_plus_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000150",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000136",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome.",
+          "xrefs" : [ "PMID:6804304" ]
         },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)A",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "cyclic translocation",
+          "val" : "autosynaptic chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37492,63 +42048,45 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cyclic_translocation"
+      "lbl" : "autosynaptic_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000725",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000134",
       "meta" : {
-        "definition" : {
-          "val" : "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "signal",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "transit peptide",
+          "val" : "sequence variant causing polypeptide fusion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "transit",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:transit_peptide",
+          "val" : "mutation causing polypeptide fusion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00055"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001616"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "transit_peptide"
+      "lbl" : "sequence_variant_causing_polypeptide_fusion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000724",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000138",
       "meta" : {
         "definition" : {
-          "val" : "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Origin_of_transfer"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "origin of transfer",
+          "val" : "homo-compound chromosome",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:oriT",
+          "val" : "homo compound chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37557,21 +42095,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "oriT"
+      "lbl" : "homo_compound_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000155",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000719",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome structure variation whereby a transposition occurred between chromosomes.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers.",
+          "xrefs" : [ "FB:WG" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)Tp",
+          "val" : "superscaffold",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "interchromosomal transposition",
+          "val" : "pseudochromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37580,21 +42119,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "interchromosomal_transposition"
+      "lbl" : "ultracontig"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000154",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000716",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication).",
+          "val" : "An mRNA that has the quality dicistronic.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insertional duplication",
+          "val" : "dicistronic mRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)Dpp",
+          "val" : "dicistronic processed transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37603,43 +42142,38 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insertional_duplication"
+      "lbl" : "dicistronic_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000721",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000715",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a dicistronic primary transcript.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A motif that is active in RNA sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with dicistronic primary transcript",
+          "val" : "RNA motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Michael, 19 nov 2004."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_dicistronic_primary_transcript"
+      "lbl" : "RNA_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000153",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000718",
       "meta" : {
         "definition" : {
-          "val" : "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons.",
+          "xrefs" : [ "SGD:rb" ]
         },
+        "comments" : [ "Term requested by Rama from SGD." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)iDp",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "inverted insertional duplication",
+          "val" : "blocked reading frame",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37648,21 +42182,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inverted_insertional_duplication"
+      "lbl" : "blocked_reading_frame"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000152",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000717",
       "meta" : {
         "definition" : {
-          "val" : "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.",
-          "xrefs" : [ "FB:reference_manual" ]
+          "val" : "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon.",
+          "xrefs" : [ "SGD:rb" ]
         },
+        "comments" : [ "This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Reading_frame"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)eDp",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "uninverted insertional duplication",
+          "val" : "reading frame",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37671,223 +42206,167 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "uninverted_insertional_duplication"
+      "lbl" : "reading_frame"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000720",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000712",
       "meta" : {
         "definition" : {
-          "val" : "A transposable element that is foreign.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene encoding a transcript that has a translational frameshift.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "foreign transposable element",
+          "val" : "gene with transcript with translational frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "requested by Michael on 19 Nov 2004."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "foreign_transposable_element"
+      "lbl" : "gene_with_transcript_with_translational_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000761",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000140",
       "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+        "definition" : {
+          "val" : "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them.",
+          "xrefs" : [ "FB:reference_manual", "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "hetero-compound chromosome",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "phagemid_clone"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000760",
-      "meta" : {
+          "pred" : "hasExactSynonym",
+          "val" : "hetero compound chromosome",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "YAC_clone"
+      "lbl" : "hetero_compound_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001607",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000711",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene with mRNA recoded by translational bypass.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "conservative amino acid substitution",
+          "val" : "gene with mRNA recoded by translational bypass",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:48:57Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conservative_amino_acid_substitution"
+      "lbl" : "gene_with_mRNA_recoded_by_translational_bypass"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000180",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000714",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_variant_effect that changes the gene structure.",
+          "val" : "A region of nucleotide sequence corresponding to a known motif.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting gene structure",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_note:nucleotide_motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting gene structure",
+          "val" : "nucleotide motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001564"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_gene_structure"
+      "lbl" : "nucleotide_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001606",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000713",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.",
+          "val" : "A motif that is active in the DNA form of the sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+          "val" : "http://en.wikipedia.org/wiki/DNA_motif"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VAAST:amino_acid_substitution",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "amino acid substitution",
+          "val" : "DNA motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:48:17Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "amino_acid_substitution"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000759",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plasmid_clone"
+      "lbl" : "DNA_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001609",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000144",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "elongated polypeptide",
+          "val" : "free duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:49:52Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "elongated_polypeptide"
+      "lbl" : "free_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001608",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000143",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres.",
+          "xrefs" : [ "FB:manual" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non conservative amino acid substitution",
+          "val" : "laevosynaptic chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:49:23Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_conservative_amino_acid_substitution"
+      "lbl" : "laevosynaptic_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000756",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000142",
       "meta" : {
         "definition" : {
-          "val" : "DNA synthesized by reverse transcriptase using RNA as a template.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "An autosynaptic chromosome carrying the two right (D = dextro) telomeres.",
+          "xrefs" : [ "FB:manual" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/CDNA"
-        } ],
+        "comments" : [ "Corrected spelling from dexstrosynaptic_chromosome to dextrosynaptic_chromosome on April 14, 2020 in response to GitHub request #447" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "complementary DNA",
+          "val" : "dextrosynaptic chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -37896,187 +42375,183 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cDNA"
+      "lbl" : "dextrosynaptic_chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000184",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000710",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant affecting splicing and causes an exon loss.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene encoding an mRNA that has the stop codon redefined as selenocysteine.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causes exon loss",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causes exon loss",
+          "val" : "gene with stop codon redefined as selenocysteine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causes_exon_loss"
+      "lbl" : "gene_with_stop_codon_redefined_as_selenocysteine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001603",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000141",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.",
+          "val" : "A chromosome that occurred by the division of a larger chromosome.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide sequence variant",
+          "val" : "chromosome fission",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:47:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_sequence_variant"
+      "lbl" : "chromosome_fission"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001602",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000126",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting transcript secondary structure",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "complex change of translational product variant",
+          "val" : "sequence variant affecting transcript secondary structure",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:46:54Z"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001596"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "complex_change_of_translational_product_variant"
+      "lbl" : "sequence_variant_affecting_transcript_secondary_structure"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000755",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000125",
       "meta" : {
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Plasmid_vector#Vectors"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plasmid vector",
+          "val" : "sequence variant causing gain of function of polypeptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing gain of function of polypeptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "gain of function of polypeptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001557"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "plasmid_vector"
+      "lbl" : "sequence_variant_causing_gain_of_function_of_polypeptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000183",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000124",
       "meta" : {
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromosome structure variation",
+          "val" : "sequence variant causing partial loss of function of polypeptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing partial loss of function of polypeptide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:CHROMOSOME_LARGE_DELETION",
+          "val" : "partial loss of function of polypeptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001561"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "chromosome_structure_variation"
+      "lbl" : "sequence_variant_causing_partial_loss_of_function_of_polypeptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001605",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000123",
       "meta" : {
-        "definition" : {
-          "val" : "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "amino acid insertion",
+          "pred" : "hasRelatedSynonym",
+          "val" : "polypeptide_post-translational_processing_affected",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:47:56Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "amino_acid_insertion"
+      "lbl" : "polypeptide_post_translational_processing_affected"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000758",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000127",
       "meta" : {
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "double stranded cDNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "double-strand cDNA",
+          "val" : "sequence variant causing compensatory transcript secondary structure mutation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "double strand cDNA",
+          "val" : "mutation causing compensatory transcript secondary structure mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001597"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "double_stranded_cDNA"
+      "lbl" : "sequence_variant_causing_compensatory_transcript_secondary_structure_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000182",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#consider",
+      "type" : "PROPERTY",
+      "lbl" : "consider"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000709",
       "meta" : {
         "definition" : {
-          "val" : "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts.",
+          "xrefs" : [ "SO:nlw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:chromosome_number_variation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "chromosome number variation",
+          "val" : "SL2 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38085,21 +42560,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosome_number_variation"
+      "lbl" : "SL2_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000757",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000708",
       "meta" : {
+        "definition" : {
+          "val" : "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs.",
+          "xrefs" : [ "SO:nlw" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "single-strand cDNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "single strand cDNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "single stranded cDNA",
+          "val" : "SL1 acceptor site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38108,74 +42579,70 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "single_stranded_cDNA"
+      "lbl" : "SL1_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000181",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000705",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene.",
+          "val" : "Two or more adjacent copies of a region (of length greater than 1).",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Tandem_repeat"
+        }, {
+          "val" : "http://www.sci.sdsu.edu/~smaloy/Glossary/T.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing gene fusion",
+          "val" : "INSDC_qualifier:tandem",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing gene fusion",
+          "pred" : "hasExactSynonym",
+          "val" : "tandem repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001565"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_gene_fusion"
+      "lbl" : "tandem_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001604",
+      "id" : "http://purl.obolibrary.org/obo/so#adjacent_to",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap.",
+          "xrefs" : [ "PMID:20226267", "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "amino acid deletion",
-          "xrefs" : [ ]
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:47:36Z"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "amino_acid_deletion"
+      "type" : "PROPERTY",
+      "lbl" : "adjacent_to"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000752",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000704",
       "meta" : {
+        "definition" : {
+          "val" : "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.",
+          "xrefs" : [ "SO:immuno_workshop" ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Gene"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene group regulatory region",
+          "val" : "INSDC_feature:gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38184,13 +42651,26 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_group_regulatory_region"
+      "lbl" : "gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000751",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000707",
       "meta" : {
+        "definition" : {
+          "val" : "The 5' five prime splice site region of the donor RNA.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "SL RNA contains a donor site." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "proviral location",
+          "val" : "trans-splice donor site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "trans splice donor site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "5 prime trans splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38199,111 +42679,98 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "proviral_location"
+      "lbl" : "trans_splice_donor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000186",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000706",
       "meta" : {
+        "definition" : {
+          "val" : "The 3' splice site of the acceptor primary transcript.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing cryptic splice donor activation",
+          "val" : "trans splice acceptor site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "3' trans splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001571"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_cryptic_splice_donor_activation"
+      "lbl" : "trans_splice_acceptor_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001601",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000701",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.",
+          "val" : "A region of sequence where the validity of the base calling is questionable.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "conformational change variant",
+          "val" : "possible base call error",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:45:48Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conformational_change_variant"
+      "lbl" : "possible_base_call_error"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000754",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000700",
       "meta" : {
         "definition" : {
-          "val" : "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.",
-          "xrefs" : [ "ISBN:0-1767-2380-8" ]
+          "val" : "A comment about the sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "lambda vector",
-          "xrefs" : [ ]
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lambda_vector"
+      "lbl" : "remark"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001600",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000703",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the resulting polypeptide structure.",
+          "val" : "A region of sequence implicated in an experimental result.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "complex 3D structural variant",
+          "val" : "experimental result region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:45:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "complex_3D_structural_variant"
+      "lbl" : "experimental_result_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000753",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000702",
       "meta" : {
         "definition" : {
-          "val" : "The region of sequence that has been inserted and is being propagated by the clone.",
+          "val" : "A region of sequence where there may have been an error in the assembly.",
           "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "clone insert",
+          "val" : "possible assembly error",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38312,46 +42779,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "clone_insert"
+      "lbl" : "possible_assembly_error"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000185",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000132",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072).",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "The effect of a change in nucleotide sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.\nUpdated after discussion with Peter Taschner - Feb 09." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causes intron gain",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causes intron gain",
+          "val" : "sequence variant effect",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causes_intron_gain"
+      "lbl" : "sequence_variant_effect"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000750",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000159",
       "meta" : {
         "definition" : {
-          "val" : "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)eTp",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "amplification origin",
+          "val" : "uninverted intrachromosomal transposition",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38360,13 +42823,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "amplification_origin"
+      "lbl" : "uninverted_intrachromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000749",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000158",
       "meta" : {
+        "definition" : {
+          "val" : "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.",
+          "xrefs" : [ "FB:reference_manual" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plasmid location",
+          "val" : "inverted intrachromosomal transposition",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)iTp",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38375,13 +42846,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plasmid_location"
+      "lbl" : "inverted_intrachromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000748",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000157",
       "meta" : {
+        "definition" : {
+          "val" : "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.",
+          "xrefs" : [ "FB:reference_manual" ]
+        },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)eTp",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "proplastid sequence",
+          "val" : "uninverted interchromosomal transposition",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38390,13 +42869,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "proplastid_sequence"
+      "lbl" : "uninverted_interchromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000745",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000156",
       "meta" : {
+        "definition" : {
+          "val" : "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment.",
+          "xrefs" : [ "FB:reference_manual" ]
+        },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)iTp",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "chloroplast sequence",
+          "val" : "inverted interchromosomal transposition",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38405,23 +42892,35 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chloroplast_sequence"
+      "lbl" : "inverted_interchromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000173",
+      "id" : "http://purl.obolibrary.org/obo/so#trans_spliced_from",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-08-19T02:22:14Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "trans_spliced_from"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000738",
       "meta" : {
         "definition" : {
-          "val" : "A duplication consisting of 2 identical adjacent regions.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA belonging to the nuclear genome of cell.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
+        "comments" : [ "Moved from is_a SO:0000736 (organelle_sequence) when brought to our attention by GitHub issue #489." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tandem duplication",
+          "val" : "nuclear sequence",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "erverted",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -38429,13 +42928,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tandem_duplication"
+      "lbl" : "nuclear_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000744",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000737",
       "meta" : {
+        "definition" : {
+          "val" : "DNA belonging to the genome of a mitochondria.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromoplast sequence",
+          "val" : "mitochondrial sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38444,25 +42948,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromoplast_sequence"
+      "lbl" : "mitochondrial_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000171",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000739",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted.",
-          "xrefs" : [ "FB:reference_manual", "SO:ke" ]
+          "val" : "DNA belonging to the genome of a plastid such as a chloroplast. The nucleomorph is the nuclei of the plastic.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "deficient inversion",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)Df",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "(Drosophila)DfIn",
+          "val" : "nucleomorphic sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38471,13 +42967,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "deficient_inversion"
+      "lbl" : "nucleomorphic_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000747",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000734",
       "meta" : {
+        "definition" : {
+          "val" : "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group.",
+          "xrefs" : [ "http://mged.sourceforge.net/ontologies/MGEDontology.php" ]
+        },
+        "comments" : [ "Added for the MO people." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "leucoplast sequence",
+          "val" : "exemplar mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38486,13 +42987,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "leucoplast_sequence"
+      "lbl" : "exemplar_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000746",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000162",
       "meta" : {
+        "definition" : {
+          "val" : "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.",
+          "xrefs" : [ "FB:reference_manual" ]
+        },
+        "comments" : [ "FLAG - definition describes an unknown." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cyanelle sequence",
+          "val" : "unorientated intrachromosomal transposition",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)uTp",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38501,13 +43011,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cyanelle_sequence"
+      "lbl" : "unoriented_intrachromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000170",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000733",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute describing a located_sequence_feature.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "uncharacterized chromosomal mutation",
+          "val" : "feature attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38516,38 +43030,46 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "uncharacterized_chromosomal_mutation"
+      "lbl" : "feature_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000741",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000161",
       "meta" : {
         "definition" : {
-          "val" : "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species.",
-          "xrefs" : [ "PMID:8395055" ]
+          "val" : "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Kinetoplast"
-        } ],
+        "comments" : [ "FLAG - term describes an unknown." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "kinetoplast_chromosome",
+          "val" : "unorientated interchromosomal transposition",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)uTp",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0000826"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "kinetoplast"
+      "lbl" : "unoriented_interchromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000740",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000160",
       "meta" : {
+        "definition" : {
+          "val" : "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded.",
+          "xrefs" : [ "FB:reference_manual" ]
+        },
+        "comments" : [ "Flag - unknown in the definition." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)uDp",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "plastid sequence",
+          "val" : "unoriented insertional duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38556,13 +43078,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plastid_sequence"
+      "lbl" : "unoriented_insertional_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000743",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000736",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence of DNA that originates from a an organelle.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "apicoplast sequence",
+          "val" : "organelle sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38571,13 +43097,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "apicoplast_sequence"
+      "lbl" : "organelle_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000175",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000735",
       "meta" : {
+        "definition" : {
+          "val" : "The location of a sequence.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "partially characterized chromosomal mutation",
+          "val" : "sequence location",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -38586,890 +43116,608 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "partially_characterized_chromosomal_mutation"
+      "lbl" : "sequence_location"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000742",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000730",
       "meta" : {
         "definition" : {
-          "val" : "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.",
-          "xrefs" : [ "PMID:8395055" ]
+          "val" : "A gap in the sequence of known length. The unknown bases are filled in with N's.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasNarrowSynonym",
+          "val" : "INSDC_feature:assembly_gap",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "maxicircle_chromosome",
+          "val" : "INSDC_feature:gap",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0000827"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "maxicircle"
+      "lbl" : "gap"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000781",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000732",
       "meta" : {
         "definition" : {
-          "val" : "Attribute describing sequence that has been integrated with foreign sequence.",
+          "val" : "An attribute describing an unverified region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Predicted"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transgenic"
+      "lbl" : "predicted"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000780",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000731",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute to describe a feature that is incomplete.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Term added because of request by MO people." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "fragment",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added by KE Jan 2006 to capture the kinds of attributes of TEs"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transposable_element_attribute"
+      "lbl" : "fragmentary"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001630",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000148",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
-        "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "snpEff:SPLICE_SITE_BRANCH_U12",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "splice region variant",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:SPLICE_SITE_REGION",
+          "val" : "(Drosophila)T",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:splicing",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:splice_region_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:splice_region_variant",
+          "val" : "(Drosophila)InT",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:splice_region_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "snpEff:SPLICE_SITE_BRANCH",
+          "val" : "inversion cum translocation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:46:02Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_region_variant"
+      "lbl" : "inversion_cum_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000783",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000147",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a region that was modified in vitro.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)Df",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "deficient translocation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)DfT",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered"
+      "lbl" : "deficient_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000782",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000146",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001784"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000145",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a feature that occurs in nature.",
+          "val" : "A ring chromosome which is a copy of another chromosome.",
           "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "free ring duplication",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)R",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "natural"
+      "lbl" : "free_ring_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#started_by",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000149",
       "meta" : {
         "definition" : {
-          "val" : "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.",
-          "xrefs" : [ "PMID:20226267" ]
+          "val" : "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)bDp",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "bipartite duplication",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T01:43:55Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: CDS started_by start_codon."
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "started_by"
+      "type" : "CLASS",
+      "lbl" : "bipartite_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001629",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000727",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs.",
+          "xrefs" : [ "PMID:19660565", "SO:SG" ]
         },
-        "xrefs" : [ {
-          "val" : "http://vat.gersteinlab.org/formats.php"
-        } ],
+        "comments" : [ "Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice site variant",
+          "val" : "CRM",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAT:spliceOverlap",
+          "val" : "transcription factor module",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "essential_splice_site",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "cis regulatory module",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TF module",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:42:00Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_site_variant"
+      "lbl" : "cis_regulatory_module"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001628",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000726",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located in the intergenic region, between genes.",
+          "val" : "The simplest repeated component of a repeat region. A single repeat.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Added to comply with the feature table. A single repeat." ],
         "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+          "val" : "http://www.insdc.org/files/feature_table.html"
         } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:intergenic",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:intergenic_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:intergenic_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "intergenic",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:INTERGENIC",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:intergenic",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "intergenic variant",
+          "val" : "repeat unit",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T05:07:37Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intergenic_variant"
+      "lbl" : "repeat_unit"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000778",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000729",
       "meta" : {
         "definition" : {
-          "val" : "A non functional descendent of a tRNA.",
+          "val" : "An attribute of protein-coding genes where the initial protein product contains an intein.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:pseudo",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "pseudogenic tRNA",
+          "val" : "intein containing",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudogenic_tRNA"
+      "lbl" : "intein_containing"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001624",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000728",
       "meta" : {
         "definition" : {
-          "val" : "A UTR variant of the 3' UTR.",
+          "val" : "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Intein-mediated protein splicing occurs after mRNA has been translated into a protein." ],
         "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+          "val" : "http://en.wikipedia.org/wiki/Intein"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:3_prime_utr_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:three_prime_UTR_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:3_prime_UTR_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "3PRIME_UTR",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:UTR3",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "3'UTR variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "untranslated-3",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:3-prime-UTR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:UTR_3_PRIME",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:3_prime_UTR_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "three prime UTR variant",
+          "val" : "protein intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T11:23:54Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term 3prime UTR variations - In 3prime UTR."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "3_prime_UTR_variant"
+      "lbl" : "intein"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000777",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000723",
       "meta" : {
         "definition" : {
-          "val" : "A non functional descendant of an rRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Genomic sequence removed from the genome, as a normal event, by a process of recombination.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:pseudo",
+          "val" : "INSDC_feature:iDNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "pseudogenic rRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:rRNA",
+          "val" : "intervening DNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudogenic_rRNA"
+      "lbl" : "iDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001627",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000151",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant occurring within an intron.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed).",
+          "xrefs" : [ "FB:reference_manual" ]
         },
-        "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:intron_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "intron variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:INTRON",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:intron-near-splice",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "intron_",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:intronic",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:intron",
+          "val" : "(Drosophila)bIn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "intronic",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:intron_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:intron_variant",
+          "val" : "bipartite inversion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Intronic variations - In intron."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T03:52:38Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intron_variant"
+      "lbl" : "bipartite_inversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000779",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000722",
       "meta" : {
         "definition" : {
-          "val" : "An episome that is engineered.",
+          "val" : "A gene that encodes a polycistronic mRNA.",
           "xrefs" : [ "SO:xp" ]
         },
+        "comments" : [ "Requested by MA nov 19 2004." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered episome",
+          "val" : "gene with dicistronic mRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "gene with dicistronic processed transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Lynn Crosby Jan 2006."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_episome"
+      "lbl" : "gene_with_dicistronic_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001626",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000150",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
-        "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "incomplete terminal codon variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "partial_codon",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:incomplete_terminal_codon_variant",
+          "val" : "cyclic translocation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T03:51:15Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_terminal_codon_variant"
+      "lbl" : "cyclic_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001621",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000725",
       "meta" : {
         "definition" : {
-          "val" : "A variant in a transcript that is the target of NMD.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle).",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
-        "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        } ],
+        "comments" : [ "Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "transit",
+          "xrefs" : [ "uniprot:feature_type" ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:NMD_transcript_variant",
+          "val" : "transit peptide",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "NMD transcript variant",
+          "pred" : "hasRelatedSynonym",
+          "val" : "signal",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "NMD_transcript",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "INSDC_feature:transit_peptide",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T11:20:40Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00055"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "NMD_transcript_variant"
+      "lbl" : "transit_peptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000774",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000724",
       "meta" : {
         "definition" : {
-          "val" : "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Origin_of_transfer"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "metabolic island",
+          "val" : "INSDC_feature:oriT",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands."
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "metabolic_island"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000773",
-      "meta" : {
-        "definition" : {
-          "val" : "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pathogenic island",
+          "val" : "origin of transfer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pathogenic_island"
+      "lbl" : "oriT"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001620",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000155",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant located with the sequence of the mature miRNA.",
+          "val" : "A chromosome structure variation whereby a transposition occurred between chromosomes.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "XX:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mature miRNA variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:MICRO_RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)Tp",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:mature_miRNA_variant",
+          "val" : "interchromosomal transposition",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "within_mature_miRNA",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T11:16:58Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Within mature miRNA - Located within a microRNA."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mature_miRNA_variant"
+      "lbl" : "interchromosomal_transposition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001623",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000154",
       "meta" : {
         "definition" : {
-          "val" : "A UTR variant of the 5' UTR.",
+          "val" : "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication).",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:UTR_5_PRIME",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:5_prime_UTR_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:five_prime_UTR_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five prime UTR variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5PRIME_UTR",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5'UTR variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:5_prime_UTR_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:5_prime_utr_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:UTR5",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "untranslated-5",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
+          "val" : "(Drosophila)Dpp",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:5-prime-UTR",
+          "val" : "insertional duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T11:23:29Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: 5prime UTR variations - In 5prime UTR (untranslated region)."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_variant"
+      "lbl" : "insertional_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000776",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000721",
       "meta" : {
         "definition" : {
-          "val" : "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that encodes a dicistronic primary transcript.",
+          "xrefs" : [ "SO:xp" ]
         },
+        "comments" : [ "Requested by Michael, 19 nov 2004." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "symbiosis island",
+          "val" : "gene with dicistronic primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "symbiosis_island"
+      "lbl" : "gene_with_dicistronic_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001622",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000153",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant that is located within the UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "UTR_",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "inverted insertional duplication",
+          "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "UTR variant",
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)iDp",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T11:22:58Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "UTR_variant"
+      "lbl" : "inverted_insertional_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000775",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000152",
       "meta" : {
         "definition" : {
-          "val" : "An adaptive island is a genomic island that provides an adaptive advantage to the host.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments.",
+          "xrefs" : [ "FB:reference_manual" ]
         },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)eDp",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "adaptive island",
+          "val" : "uninverted insertional duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "adaptive_island"
+      "lbl" : "uninverted_insertional_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000770",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000720",
       "meta" : {
         "definition" : {
-          "val" : "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.",
-          "xrefs" : [ "Indiana:kw", "doi:10.1093/nar/gkh795" ]
+          "val" : "A transposable element that is foreign.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "requested by Michael on 19 Nov 2004." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tmRNA acceptor piece",
+          "val" : "foreign transposable element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added in response to Kelly Williams from Indiana. Date: Nov 2005."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tmRNA_acceptor_piece"
+      "lbl" : "foreign_transposable_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000772",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000761",
       "meta" : {
-        "definition" : {
-          "val" : "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.",
-          "xrefs" : [ "Phigo:at", "SO:ke" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Genomic_island"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "genomic island",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Genomic islands are transmissible elements characterized by large size (>10kb)."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "genomic_island"
+      "lbl" : "phagemid_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000771",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000179",
       "meta" : {
-        "definition" : {
-          "val" : "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.",
-          "xrefs" : [ "http://rgd.mcw.edu/tu/qtls/" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "quantitative trait locus",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added in respose to request by Simon Twigger November 14th 2005."
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_1000049"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000760",
+      "meta" : {
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "QTL"
+      "lbl" : "YAC_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001618",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001607",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.",
+          "val" : "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inactive catalytic site",
+          "val" : "conservative amino acid substitution",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -39480,171 +43728,149 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T03:06:14Z"
+          "val" : "2010-03-22T02:48:57Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inactive_catalytic_site"
+      "lbl" : "conservative_amino_acid_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001617",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000180",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant of the CD that causes a truncation of the resulting polypeptide.",
+          "val" : "A sequence_variant_effect that changes the gene structure.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting gene structure",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide truncation",
+          "val" : "sequence variant affecting gene structure",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001564"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:53:07Z"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_truncation"
+      "lbl" : "sequence_variant_affecting_gene_structure"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001619",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001606",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant of a non coding RNA gene.",
+          "val" : "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
         } ],
         "synonyms" : [ {
-          "pred" : "hasNarrowSynonym",
-          "val" : "ANNOVAR:ncRNA",
-          "xrefs" : [ "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nc transcript variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non coding transcript variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "within_non_coding_gene",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:non_coding_transcript_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "VAAST:amino_acid_substitution",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:non_coding_transcript_variant",
+          "val" : "amino acid substitution",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T11:16:23Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2010-03-22T02:48:17Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Within non-coding gene - Located within a gene that does not code for a protein."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_coding_transcript_variant"
+      "lbl" : "amino_acid_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000767",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000759",
       "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "clone_insert_start"
+      "lbl" : "plasmid_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001614",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001609",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.",
+          "val" : "An elongation of a polypeptide sequence deriving from a sequence variant extending the CDS.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "elongated in frame polypeptide N terminal",
+          "val" : "elongated polypeptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:51:49Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2010-03-22T02:49:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "elongated_in_frame_polypeptide_N_terminal_elongation"
+      "lbl" : "elongated_polypeptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001613",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001608",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.",
+          "val" : "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "elongated polypeptide out of frame C terminal",
+          "val" : "non conservative amino acid substitution",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:49:23Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:51:20Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "elongated_out_of_frame_polypeptide_C_terminal"
+      "lbl" : "non_conservative_amino_acid_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000766",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000756",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA synthesized by reverse transcriptase using RNA as a template.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/CDNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pyrrolysyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "pyrrolysyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "pyrrolysyl tRNA",
+          "val" : "complementary DNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -39653,299 +43879,328 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pyrrolysyl_tRNA"
+      "lbl" : "cDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000769",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001603",
       "meta" : {
         "definition" : {
-          "val" : "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.",
-          "xrefs" : [ "Indiana:kw", "doi:10.1093/nar/gkh795", "issn:1362-4962" ]
+          "val" : "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tmRNA coding piece",
+          "val" : "polypeptide sequence variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added in response to comment from Kelly Williams from Indiana. Nov 2005."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:47:13Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tmRNA_coding_piece"
+      "lbl" : "polypeptide_sequence_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001616",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000184",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes a fusion of two polypeptide sequences.",
+          "val" : "A sequence variant affecting splicing and causes an exon loss.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide fusion",
+          "val" : "sequence variant causes exon loss",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causes exon loss",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:52:43Z"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_fusion"
+      "lbl" : "sequence_variant_causes_exon_loss"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001615",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000183",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An alteration of the genome that leads to a change in the structure or number of one or more chromosomes.",
+          "xrefs" : [ ]
         },
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "elongated out of frame N terminal",
+          "val" : "snpEff:CHROMOSOME_LARGE_DELETION",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "chromosome structure variation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:52:05Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "elongated_out_of_frame_polypeptide_N_terminal"
+      "lbl" : "chromosome_structure_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000768",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000755",
       "meta" : {
         "definition" : {
-          "val" : "A plasmid that may integrate with a chromosome.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A plasmid that has been generated to act as a vector for foreign sequence.",
+          "xrefs" : [ ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Plasmid_vector#Vectors"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "plasmid vector",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "episome"
+      "lbl" : "plasmid_vector"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001610",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001602",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A variant that changes the translational product with respect to the reference.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "elongated polypeptide C terminal",
+          "val" : "complex change of translational product variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:50:20Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "elongated_polypeptide_C_terminal"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000763",
-      "meta" : {
-        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:46:54Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "fosmid_clone"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#hasScope",
-      "type" : "PROPERTY",
-      "lbl" : "has_scope"
+      "lbl" : "complex_change_of_translational_product_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000762",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000758",
       "meta" : {
+        "definition" : {
+          "val" : "DNA synthesized from RNA by reverse transcriptase that has been copied by PCR to make it double stranded.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "P1_clone",
+          "val" : "double strand cDNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "double stranded cDNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "double-strand cDNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "PAC_clone"
+      "lbl" : "double_stranded_cDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001612",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001605",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.",
+          "val" : "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "elongated in frame polypeptide C terminal",
+          "val" : "amino acid insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:47:56Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:51:05Z"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "elongated_in_frame_polypeptide_C_terminal"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000765",
-      "meta" : {
-        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cosmid_clone"
+      "lbl" : "amino_acid_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001611",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000182",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus.",
+          "val" : "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "elongated polypeptide N terminal",
+          "val" : "chromosome number variation",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:chromosome_number_variation",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:50:31Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "elongated_polypeptide_N_terminal"
+      "lbl" : "chromosome_number_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000764",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000757",
       "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+        "definition" : {
+          "val" : "DNA synthesized from RNA by reverse transcriptase, single stranded.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "single strand cDNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "single-strand cDNA",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "single stranded cDNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "BAC_clone"
+      "lbl" : "single_stranded_cDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001650",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000181",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which does not cause a disruption of the translational reading frame.",
+          "val" : "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:nonframeshift substitution",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "inframe variant",
+          "val" : "mutation causing gene fusion",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:nonframeshift block substitution",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "cds-indel",
+          "val" : "sequence variant causing gene fusion",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001565"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "sequence_variant_causing_gene_fusion"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001604",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VAAST:inframe_variant",
+          "val" : "amino acid deletion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-07-19T01:24:44Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:47:36Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inframe_variant"
+      "lbl" : "amino_acid_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000321",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000752",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA with a plus 1 frameshift.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that is involved in the regulation of transcription of a group of regulated genes.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Merged into transcriptional_cis_regulatory_region (SO:0001055) on 11 Feb 2021 as part of GREEKC reducing redundancy as we prepare to submit several terms to Ensembl. See GitHub Issue #529." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mRNA with plus 1 frameshift",
+          "val" : "gene group regulatory region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001055"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_with_plus_1_frameshift"
+      "lbl" : "gene_group_regulatory_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000320",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000751",
       "meta" : {
         "definition" : {
-          "val" : "Sequences within the intron that modulate splice site selection for some introns.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The location of DNA that has come from a viral origin.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "intronic splice enhancer",
+          "val" : "proviral location",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -39954,21 +44209,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intronic_splice_enhancer"
+      "lbl" : "proviral_location"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000319",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000754",
       "meta" : {
         "definition" : {
-          "val" : "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome.",
+          "xrefs" : [ "ISBN:0-1767-2380-8" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Stop_codon"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "stop codon",
+          "val" : "lambda vector",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -39977,82 +44228,88 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stop_codon"
+      "lbl" : "lambda_vector"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001647",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001601",
       "meta" : {
         "definition" : {
-          "val" : "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.",
+          "val" : "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Kozak_consensus_sequence"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "kozak sequence",
+          "val" : "conformational change variant",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "kozak consensus sequence",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:45:48Z"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "conformational_change_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000186",
+      "meta" : {
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "kozak consensus",
+          "val" : "sequence variant causing cryptic splice donor activation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-06-07T03:12:20Z"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001571"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "kozak_sequence"
+      "lbl" : "sequence_variant_causing_cryptic_splice_donor_activation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000316",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000185",
       "meta" : {
         "definition" : {
-          "val" : "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072).",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "coding sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:CDS",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causes intron gain",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "coding_sequence",
+          "val" : "sequence variant causes intron gain",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "CDS"
+      "lbl" : "sequence_variant_causes_intron_gain"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000799",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000753",
       "meta" : {
         "definition" : {
-          "val" : "A transposable_element that is engineered and foreign.",
-          "xrefs" : [ "FB:mc" ]
+          "val" : "The region of sequence that has been inserted and is being propagated by the clone.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered foreign transposable element",
+          "val" : "clone insert",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -40061,55 +44318,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_foreign_transposable_element"
+      "lbl" : "clone_insert"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001646",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001600",
       "meta" : {
         "definition" : {
-          "val" : "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.",
+          "val" : "A sequence variant that changes the resulting polypeptide structure.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DArT marker",
+          "val" : "complex 3D structural variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:45:13Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-05-28T02:34:43Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DArT_marker"
+      "lbl" : "complex_3D_structural_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000315",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000750",
       "meta" : {
         "definition" : {
-          "val" : "The first base where RNA polymerase begins to synthesize the RNA transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcription_start_site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_feature",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:transcription_start_site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "transcription start site",
+          "val" : "amplification origin",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -40118,58 +44362,36 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TSS"
+      "lbl" : "amplification_origin"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001649",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000749",
       "meta" : {
         "definition" : {
-          "val" : "A repeat that is disrupted by the insertion of another element.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The location of DNA that has come from a plasmid sequence.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:nested",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nested repeat",
+          "val" : "plasmid location",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-06-23T03:24:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nested_repeat"
+      "lbl" : "plasmid_location"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000318",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000748",
       "meta" : {
         "definition" : {
-          "val" : "First codon to be translated by a ribosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA belonging to the genome of a proplastid such as an immature chloroplast.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Start_codon"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "initiation codon",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "start codon",
+          "val" : "proplastid sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -40178,86 +44400,80 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "start_codon"
+      "lbl" : "proplastid_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001648",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000745",
       "meta" : {
         "definition" : {
-          "val" : "A transposon that is disrupted by the insertion of another element.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA belonging to the genome of a chloroplast, a green plastid for photosynthesis.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nested transposon",
+          "val" : "chloroplast sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-06-23T03:22:57Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nested_transposon"
+      "lbl" : "chloroplast_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000317",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000173",
       "meta" : {
         "definition" : {
-          "val" : "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.",
-          "xrefs" : [ "http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html" ]
+          "val" : "A duplication consisting of 2 identical adjacent regions.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cDNA clone",
+          "val" : "tandem duplication",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "erverted",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbvar"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cDNA_clone"
+      "lbl" : "tandem_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000796",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000744",
       "meta" : {
         "definition" : {
-          "val" : "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.",
-          "xrefs" : [ "FB:mc" ]
+          "val" : "DNA belonging to the genome of a chromoplast, a colored plastid for synthesis and storage of pigments.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transgenic transposable element",
+          "val" : "chromoplast sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Modified as requested by Lynn - FB. May 2007."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transgenic_transposable_element"
+      "lbl" : "chromoplast_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000312",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000747",
       "meta" : {
         "definition" : {
-          "val" : "Attribute to describe a feature that has been experimentally verified.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA belonging to the genome of a leucoplast, a colorless plastid generally containing starch or oil.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "experimentally determined",
+          "val" : "leucoplast sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -40266,149 +44482,120 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "experimentally_determined"
+      "lbl" : "leucoplast_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001643",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000171",
       "meta" : {
         "definition" : {
-          "val" : "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted.",
+          "xrefs" : [ "FB:reference_manual", "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://en.wikipedia.org/wiki/Telomerase_RNA_component"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "Telomerase RNA component",
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)DfIn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "telomerase RNA gene",
+          "val" : "deficient inversion",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "TERC",
+          "pred" : "hasRelatedSynonym",
+          "val" : "(Drosophila)Df",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-05-18T05:26:38Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "telomerase_RNA_gene"
+      "lbl" : "deficient_inversion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001642",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000170",
       "meta" : {
         "definition" : {
-          "val" : "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.",
-          "xrefs" : [ "SO:jestill" ]
+          "val" : "A chromosome structure variant that has not been characterized.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mathematically defined repeat",
+          "val" : "uncharacterized chromosomal mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-05-03T11:50:14Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.)."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mathematically_defined_repeat"
+      "lbl" : "uncharacterized_chromosomal_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000311",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000746",
       "meta" : {
         "definition" : {
-          "val" : ".",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "DNA belonging to the genome of a cyanelle, a photosynthetic plastid found in algae.",
+          "xrefs" : [ ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "cyanelle sequence",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "similar to:<sequence_id>"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "computed_feature_by_similarity"
+      "lbl" : "cyanelle_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000795",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000741",
       "meta" : {
         "definition" : {
-          "val" : "A mini_gene that rescues.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species.",
+          "xrefs" : [ "PMID:8395055" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Kinetoplast"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rescue mini-gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "rescue mini gene",
+          "val" : "kinetoplast_chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0000826"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rescue_mini_gene"
+      "lbl" : "kinetoplast"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001645",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000177",
       "meta" : {
-        "definition" : {
-          "val" : "A measurable sequence feature that varies within a population.",
-          "xrefs" : [ "SO:db" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "genetic marker",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-05-28T02:33:07Z"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_1000049"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "genetic_marker"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000798",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000740",
       "meta" : {
         "definition" : {
-          "val" : "TE that has been modified by manipulations in vitro.",
-          "xrefs" : [ "FB:mc" ]
+          "val" : "DNA belonging to the genome of a plastid such as a chloroplast.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered transposable element",
+          "val" : "plastid sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -40417,29 +44604,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_transposable_element"
+      "lbl" : "plastid_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000314",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000743",
       "meta" : {
         "definition" : {
-          "val" : "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA belonging to the genome of an apicoplast, a non-photosynthetic plastid.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Direct_repeat"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:direct",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "direct repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "val" : "apicoplast sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -40448,222 +44623,160 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "direct_repeat"
+      "lbl" : "apicoplast_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000313",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000175",
       "meta" : {
         "definition" : {
-          "val" : "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A chromosome structure variant that has not been characterized fully.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Stem_loop"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "stem loop",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "stem-loop",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RNA_hairpin_loop",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:stem_loop",
+          "val" : "partially characterized chromosomal mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0000019"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stem_loop"
+      "lbl" : "partially_characterized_chromosomal_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000797",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000742",
       "meta" : {
         "definition" : {
-          "val" : "TE that exists (or existed) in nature.",
-          "xrefs" : [ "FB:mc" ]
+          "val" : "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method.",
+          "xrefs" : [ "PMID:8395055" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "natural transposable element",
+          "val" : "maxicircle_chromosome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0000827"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "natural_transposable_element"
+      "lbl" : "maxicircle"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001644",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000781",
       "meta" : {
         "definition" : {
-          "val" : "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.",
-          "xrefs" : [ "MGD:tm", "PMID:10354467" ]
+          "val" : "Attribute describing sequence that has been integrated with foreign sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "targeting vector",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-05-28T02:05:25Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "targeting_vector"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000792",
-      "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cloned_cDNA"
+      "lbl" : "transgenic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000791",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000780",
       "meta" : {
+        "comments" : [ "Added by KE Jan 2006 to capture the kinds of attributes of TEs" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "cloned_genomic"
+      "lbl" : "transposable_element_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000794",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001630",
       "meta" : {
         "definition" : {
-          "val" : "A rescue region that is engineered.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
         },
+        "comments" : [ "EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron." ],
+        "xrefs" : [ {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        }, {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered rescue segment",
-          "xrefs" : [ ]
+          "val" : "VAAST:splice_region_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "snpEff:SPLICE_SITE_BRANCH_U12",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "snpEff:SPLICE_SITE_BRANCH",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:splicing",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "engineered rescue fragment",
-          "xrefs" : [ ]
+          "val" : "Jannovar:splice_region_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "engineered rescue region",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "engineered_rescue_region"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001641",
-      "meta" : {
-        "definition" : {
-          "val" : "A gene that encodes a long, intervening non-coding RNA.",
-          "xrefs" : [ "PMID:23463798", "SO:ke", "http://www.gencodegenes.org/gencode_biotypes.html" ]
-        },
-        "synonyms" : [ {
+          "val" : "snpEff:SPLICE_SITE_REGION",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "lincRNA gene",
-          "xrefs" : [ ]
+          "val" : "VEP:splice_region_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splice region variant",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-21T10:14:24Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2010-03-24T09:46:02Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "lincRNA_gene"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000310",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "predicted_ab_initio_computation"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000793",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_DNA"
+      "lbl" : "splice_region_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001640",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000783",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a RNase_MRP_RNA.",
+          "val" : "An attribute to describe a region that was modified in vitro.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "RNase MRP RNA gene",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-21T10:13:58Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNase_MRP_RNA_gene"
+      "lbl" : "engineered"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000790",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000782",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a feature that is invalidated.",
+          "val" : "An attribute describing a feature that occurs in nature.",
           "xrefs" : [ "SO:ke" ]
         },
         "basicPropertyValues" : [ {
@@ -40672,212 +44785,351 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "invalidated"
+      "lbl" : "natural"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000309",
+      "id" : "http://purl.obolibrary.org/obo/so#started_by",
       "meta" : {
+        "definition" : {
+          "val" : "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary.",
+          "xrefs" : [ "PMID:20226267" ]
+        },
+        "comments" : [ "Example: CDS started_by start_codon." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T01:43:55Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "computed_feature"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000308",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "sequence_feature_locating_method"
+      "type" : "PROPERTY",
+      "lbl" : "started_by"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001639",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001629",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes an RNase P RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript.",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
         },
+        "comments" : [ "EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger." ],
+        "xrefs" : [ {
+          "val" : "http://vat.gersteinlab.org/formats.php"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNase P RNA gene",
+          "val" : "splice site variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "essential_splice_site",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAT:spliceOverlap",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-21T10:13:23Z"
+          "val" : "2010-03-24T09:42:00Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNase_P_RNA_gene"
+      "lbl" : "splice_site_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001636",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001628",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located within 2KB 5' of a gene.",
+          "val" : "A sequence variant located in the intergenic region, between genes.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript." ],
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        }, {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "near-gene-5",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
+          "val" : "Jannovar:intergenic_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "2KB upstream variant",
+          "val" : "VEP:intergenic_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "intergenic",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:intergenic",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "intergenic variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:INTERGENIC",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:intergenic",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:51:22Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-23T05:07:37Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "2KB_upstream_variant"
+      "lbl" : "intergenic_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000305",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001625",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001590"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000778",
       "meta" : {
         "definition" : {
-          "val" : "A modified nucleotide, i.e. a nucleotide other than A, T, C. G.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A non functional descendent of a tRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:modified_base",
+          "val" : "INSDC_qualifier:pseudo",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:tRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "modified base site",
+          "val" : "pseudogenic tRNA",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Modified base:<modified_base>."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "modified_DNA_base"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000789",
-      "meta" : {
-        "definition" : {
-          "val" : "An attribute to describe a feature that has been proven.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "validated"
+      "lbl" : "pseudogenic_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001635",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001624",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located within 5KB 5' of a gene.",
+          "val" : "A UTR variant of the 3' UTR.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term 3prime UTR variations - In 3prime UTR." ],
         "xrefs" : [ {
           "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        } ],
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        }, {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:upstream-gene",
-          "xrefs" : [ ]
+          "val" : "untranslated-3",
+          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbsnp"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "upstream",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "snpEff:UTR_3_PRIME",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5kb upstream variant",
+          "val" : "VAAST:three_prime_UTR_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3'UTR variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "three prime UTR variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:3_prime_UTR_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:3_prime_UTR_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:3-prime-UTR",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:UTR3",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3PRIME_UTR",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:3_prime_utr_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-23T11:23:54Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:51:06Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5KB_upstream_variant"
+      "lbl" : "3_prime_UTR_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000304",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000777",
       "meta" : {
         "definition" : {
-          "val" : "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.",
-          "xrefs" : [ "http://www.promega.com" ]
+          "val" : "A non functional descendant of an rRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+        "comments" : [ "Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:rRNA",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "type_II_enzyme_restriction_site"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000788",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:pseudo",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "pseudogenic rRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cloned"
+      "lbl" : "pseudogenic_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001638",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001627",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes for an piwi associated RNA.",
+          "val" : "A transcript variant occurring within an intron.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term: Intronic variations - In intron." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        }, {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "piRNA gene",
+          "val" : "intron variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:intron_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:INTRON",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "intronic",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:intron",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:intron_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:intronic",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:intron_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "Seattleseq:intron-near-splice",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "intron_",
+          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbsnp"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-21T10:11:36Z"
+          "val" : "2010-03-23T03:52:38Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -40887,89 +45139,119 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "piRNA_gene"
+      "lbl" : "intron_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000307",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001626",
       "meta" : {
         "definition" : {
-          "val" : "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.",
-          "xrefs" : [ "SO:rd" ]
+          "val" : "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown." ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/CpG_island"
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CG island",
+          "val" : "incomplete terminal codon variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "CpG island",
-          "xrefs" : [ ]
+          "val" : "partial_codon",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:incomplete_terminal_codon_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-23T03:51:15Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CpG_island"
+      "lbl" : "incomplete_terminal_codon_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001637",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000779",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes for ribosomal RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An episome that is engineered.",
+          "xrefs" : [ "SO:xp" ]
         },
+        "comments" : [ "Requested by Lynn Crosby Jan 2006." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rDNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "rRNA gene",
+          "val" : "engineered episome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-21T10:10:32Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_gene"
+      "lbl" : "engineered_episome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000306",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001621",
       "meta" : {
         "definition" : {
-          "val" : "A nucleotide modified by methylation.",
+          "val" : "A variant in a transcript that is the target of nonsense-mediated mRNA decay.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "methylated base feature",
+          "val" : "NMD transcript variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "NMD_transcript",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:NMD_transcript_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Nonsense mediated decay transcript variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-23T11:20:40Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "methylated_DNA_base_feature"
+      "lbl" : "NMD_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000301",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000774",
       "meta" : {
+        "definition" : {
+          "val" : "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vertebrate immune system gene recombination feature",
+          "val" : "metabolic island",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -40978,137 +45260,166 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immune_system_gene_recombination_feature"
+      "lbl" : "metabolic_island"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001632",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001620",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located 3' of a gene.",
+          "val" : "A transcript variant located with the sequence of the mature miRNA.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term: Within mature miRNA - Located within a microRNA." ],
         "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
           "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "XX:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:downstream_gene_variant",
+          "val" : "mature miRNA variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:DOWNSTREAM",
-          "xrefs" : [ ]
+          "val" : "within_mature_miRNA",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "downstream gene variant",
-          "xrefs" : [ ]
+          "val" : "snpEff:MICRO_RNA",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:downstream_gene_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:downstream",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
+          "val" : "VEP:mature_miRNA_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:49:38Z"
+          "val" : "2010-03-23T11:16:58Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "downstream_gene_variant"
+      "lbl" : "mature_miRNA_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000785",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000773",
       "meta" : {
+        "definition" : {
+          "val" : "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cloned segment",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "cloned region",
+          "val" : "pathogenic island",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cloned_region"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym",
-      "type" : "PROPERTY",
-      "lbl" : "has_narrow_synonym"
+      "lbl" : "pathogenic_island"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001631",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001623",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located 5' of a gene.",
+          "val" : "A UTR variant of the 5' UTR.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term: 5prime UTR variations - In 5prime UTR (untranslated region)." ],
         "xrefs" : [ {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         }, {
           "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:upstream_gene_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "Seattleseq:5-prime-UTR",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:upstream_gene_variant",
-          "xrefs" : [ ]
+          "val" : "Jannovar:5_prime_utr_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:UTR5",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:UPSTREAM",
+          "val" : "VEP:5_prime_UTR_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime UTR variant",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:upstream",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:5_prime_UTR_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "upstream gene variant",
+          "val" : "snpEff:UTR_5_PRIME",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5PRIME_UTR",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "untranslated-5",
+          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbsnp"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:five_prime_UTR_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5'UTR variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:49:13Z"
+          "val" : "2010-03-23T11:23:29Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "upstream_gene_variant"
+      "lbl" : "5_prime_UTR_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000300",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000776",
       "meta" : {
+        "definition" : {
+          "val" : "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "recombination feature of rearranged gene",
+          "val" : "symbiosis island",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -41117,223 +45428,247 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombination_feature_of_rearranged_gene"
+      "lbl" : "symbiosis_island"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000784",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000775",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe a region from another species.",
+          "val" : "An adaptive island is a genomic island that provides an adaptive advantage to the host.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "adaptive island",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "foreign"
+      "lbl" : "adaptive_island"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001634",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001622",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located within a half KB of the end of a gene.",
+          "val" : "A transcript variant that is located within the UTR.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "500B downstream variant",
-          "xrefs" : [ ]
+          "val" : "UTR_",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "near-gene-3",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
+          "val" : "UTR variant",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:50:42Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-23T11:22:58Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "500B_downstream_variant"
+      "lbl" : "UTR_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000303",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000770",
       "meta" : {
         "definition" : {
-          "val" : "Part of the primary transcript that is clipped off during processing.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.",
+          "xrefs" : [ "Indiana:kw", "doi:10.1093/nar/gkh795" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "clip"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000787",
-      "meta" : {
+        "comments" : [ "Added in response to Kelly Williams from Indiana. Date: Nov 2005." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "tmRNA acceptor piece",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "clone_attribute"
+      "lbl" : "tmRNA_acceptor_piece"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001633",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000772",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located within 5 KB of the end of a gene.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.",
+          "xrefs" : [ "Phigo:at", "SO:ke" ]
         },
+        "comments" : [ "Genomic islands are transmissible elements characterized by large size (>10kb)." ],
         "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+          "val" : "http://en.wikipedia.org/wiki/Genomic_island"
         } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "within 5KB downstream",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5KB downstream variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "downstream",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:downstream-gene",
+          "val" : "genomic island",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-24T09:50:16Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5KB_downstream_variant"
+      "lbl" : "genomic_island"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000786",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000771",
       "meta" : {
+        "definition" : {
+          "val" : "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.",
+          "xrefs" : [ "http://rgd.mcw.edu/tu/qtls/" ]
+        },
+        "comments" : [ "Added in respose to request by Simon Twigger November 14th 2005." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "reagent attribute",
+          "val" : "quantitative trait locus",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added jan 2006 by KE."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reagent_attribute"
+      "lbl" : "QTL"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000302",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001618",
       "meta" : {
         "definition" : {
-          "val" : "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.",
-          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
+          "val" : "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "J-RS",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "J gene recombination feature",
+          "val" : "inactive catalytic site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T03:06:14Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "J_gene_recombination_feature"
+      "lbl" : "inactive_catalytic_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001672",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001617",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant of the CD that causes a truncation of the resulting polypeptide.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bacterial RNA polymerase promoter sigma54",
+          "val" : "polypeptide truncation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:53:07Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-06T01:42:37Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bacterial_RNApol_promoter_sigma54"
+      "lbl" : "polypeptide_truncation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000341",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001619",
       "meta" : {
         "definition" : {
-          "val" : "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A transcript variant of a non coding RNA gene.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Within non-coding gene - Located within a gene that does not code for a protein." ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Cytological_band"
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cytological band",
-          "xrefs" : [ ]
+          "val" : "within_non_coding_gene",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbsnp"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "chromosome band",
+          "val" : "VEP:non_coding_transcript_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:non_coding_transcript_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "nc transcript variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "cytoband",
+          "val" : "non coding transcript variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "ANNOVAR:ncRNA",
+          "xrefs" : [ "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-23T11:16:23Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosome_band"
+      "lbl" : "non_coding_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001671",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000767",
       "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "clone_insert_start"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001614",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bacterial RNA polymerase promoter sigma 70",
+          "val" : "elongated in frame polypeptide N terminal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -41341,344 +45676,414 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-06T01:41:34Z"
+          "val" : "2010-03-22T02:51:49Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bacterial_RNApol_promoter_sigma_70"
+      "lbl" : "elongated_in_frame_polypeptide_N_terminal_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000340",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001613",
       "meta" : {
         "definition" : {
-          "val" : "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Chromosome"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "elongated polypeptide out of frame C terminal",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:51:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosome"
+      "lbl" : "elongated_out_of_frame_polypeptide_C_terminal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001674",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000766",
       "meta" : {
         "definition" : {
-          "val" : "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.",
-          "xrefs" : [ "PMID:18331472" ]
+          "val" : "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "minus 24 signal",
+          "pred" : "hasExactSynonym",
+          "val" : "pyrrolysyl tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "pyrrolysyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "pyrrolysyl-transfer ribonucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-06T01:45:24Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_24_signal"
+      "lbl" : "pyrrolysyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000343",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000769",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together.",
+          "xrefs" : [ "Indiana:kw", "doi:10.1093/nar/gkh795", "issn:1362-4962" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Added in response to comment from Kelly Williams from Indiana. Nov 2005." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "tmRNA coding piece",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "match"
+      "lbl" : "tmRNA_coding_piece"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001673",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001616",
       "meta" : {
         "definition" : {
-          "val" : "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.",
-          "xrefs" : [ "PMID:18331472" ]
+          "val" : "A sequence variant that causes a fusion of two polypeptide sequences.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "minus 12 signal",
+          "val" : "polypeptide fusion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:52:43Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-06T01:44:57Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_12_signal"
+      "lbl" : "polypeptide_fusion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000342",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000768",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "site specific recombination target region",
-          "xrefs" : [ ]
-        } ],
+        "definition" : {
+          "val" : "A plasmid that may integrate with a chromosome.",
+          "xrefs" : [ "SO:ma" ]
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "site_specific_recombination_target_region"
+      "lbl" : "episome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001670",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001615",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "distal promoter element",
+          "pred" : "hasExactSynonym",
+          "val" : "elongated out of frame N terminal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T03:21:08Z"
+          "val" : "2010-03-22T02:52:05Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "distal_promoter_element"
+      "lbl" : "elongated_out_of_frame_polypeptide_N_terminal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001669",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001610",
       "meta" : {
         "definition" : {
-          "val" : "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.",
-          "xrefs" : [ "PMID:16858867" ]
+          "val" : "An elongation of a polypeptide sequence at the C terminus deriving from a sequence variant extending the CDS.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNApol II core promoter",
+          "val" : "elongated polypeptide C terminal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T03:13:41Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:50:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNApol_II_core_promoter"
+      "lbl" : "elongated_polypeptide_C_terminal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000338",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000763",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "fosmid_clone"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasScope",
+      "type" : "PROPERTY",
+      "lbl" : "has_scope"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000762",
       "meta" : {
-        "definition" : {
-          "val" : "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.",
-          "xrefs" : [ "http://www.pnas.org/cgi/content/full/97/18/10083" ]
-        },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "miniature inverted repeat transposable element",
+          "pred" : "hasRelatedSynonym",
+          "val" : "P1_clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "MITE"
+      "lbl" : "PAC_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001668",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001612",
       "meta" : {
         "definition" : {
-          "val" : "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor).",
-          "xrefs" : [ "PMID:12515390", "PMID:9679020", "SO:ml" ]
+          "val" : "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "proximal promoter element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "specific transcription factor binding site",
+          "pred" : "hasExactSynonym",
+          "val" : "elongated in frame polypeptide C terminal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T03:10:23Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:51:05Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "proximal_promoter_element"
+      "lbl" : "elongated_in_frame_polypeptide_C_terminal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000337",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000765",
       "meta" : {
-        "definition" : {
-          "val" : "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.",
-          "xrefs" : [ "SO:rd" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "RNAi reagent",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "RNAi_reagent"
+      "lbl" : "cosmid_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000339",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001611",
       "meta" : {
         "definition" : {
-          "val" : "A region in a genome which promotes recombination.",
-          "xrefs" : [ "SO:rd" ]
+          "val" : "An elongation of a polypeptide sequence at the N terminus deriving from a sequence variant extending the CDS.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Recombination_hotspot"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "recombination hotspot",
+          "val" : "elongated polypeptide N terminal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:50:31Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombination_hotspot"
+      "lbl" : "elongated_polypeptide_N_terminal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000334",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000764",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "BAC_clone"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001650",
       "meta" : {
         "definition" : {
-          "val" : "Non-coding region of sequence similarity by descent from a common ancestor.",
+          "val" : "A sequence variant which does not cause a disruption of the translational reading frame.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "noncoding conserved region",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:nonframeshift substitution",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:nonframeshift block substitution",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conserved non-coding element",
-          "xrefs" : [ ]
+          "val" : "cds-indel",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbsnp"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nc conserved region",
-          "xrefs" : [ ]
+          "val" : "VAAST:inframe_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conserved non-coding sequence",
+          "val" : "inframe variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-07-19T01:24:44Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nc_conserved_region"
+      "lbl" : "inframe_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001665",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000321",
       "meta" : {
         "definition" : {
-          "val" : "A sub element of the DCE core promoter element, with consensus sequence CTTC.",
-          "xrefs" : [ "PMID:16858867", "SO:ke" ]
+          "val" : "An mRNA with a plus 1 frameshift.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "DCE SI",
+          "pred" : "hasExactSynonym",
+          "val" : "mRNA with plus 1 frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T03:00:10Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DCE_SI"
+      "lbl" : "mRNA_with_plus_1_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001664",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001652",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001822"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001651",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001821"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000320",
       "meta" : {
         "definition" : {
-          "val" : "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII.",
-          "xrefs" : [ "PMID:16858867" ]
+          "val" : "Sequences within the intron that modulate splice site selection for some introns.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "downstream core element",
+          "pred" : "hasExactSynonym",
+          "val" : "intronic splice enhancer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T02:56:41Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DCE"
+      "lbl" : "intronic_splice_enhancer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000333",
+      "id" : "http://purl.obolibrary.org/obo/BS_00331",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000839"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000319",
       "meta" : {
         "definition" : {
-          "val" : "The boundary between two exons in a processed transcript.",
+          "val" : "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis.",
           "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Stop_codon"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "exon junction",
+          "val" : "stop codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -41687,121 +46092,132 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exon_junction"
+      "lbl" : "stop_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000336",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001647",
       "meta" : {
         "definition" : {
-          "val" : "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog).",
-          "xrefs" : [ "http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html" ]
+          "val" : "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Pseudogene"
+          "val" : "http://en.wikipedia.org/wiki/Kozak_consensus_sequence"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:unknown",
+          "val" : "kozak sequence",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:gene",
+          "pred" : "hasExactSynonym",
+          "val" : "kozak consensus",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:pseudo",
+          "val" : "kozak consensus sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-06-07T03:12:20Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudogene"
+      "lbl" : "kozak_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001667",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000316",
       "meta" : {
         "definition" : {
-          "val" : "A sub element of the DCE core promoter element with consensus sequence AGC.",
-          "xrefs" : [ "PMID:16858867", "SO:ke" ]
+          "val" : "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DCE SIII",
+          "val" : "coding_sequence",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T03:00:44Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:CDS",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "coding sequence",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DCE_SIII"
+      "lbl" : "CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001666",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000799",
       "meta" : {
         "definition" : {
-          "val" : "A sub element of the DCE core promoter element with consensus sequence CTGT.",
-          "xrefs" : [ "PMID:16858867", "SO:ke" ]
+          "val" : "A transposable_element that is engineered and foreign.",
+          "xrefs" : [ "FB:mc" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DCE SII",
+          "val" : "engineered foreign transposable element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T03:00:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DCE_SII"
+      "lbl" : "engineered_foreign_transposable_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000335",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001646",
       "meta" : {
         "definition" : {
-          "val" : "A mRNA with a minus 2 frameshift.",
+          "val" : "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mRNA with minus 2 frameshift",
+          "val" : "DArT marker",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-05-28T02:34:43Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_with_minus_2_frameshift"
+      "lbl" : "DArT_marker"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000330",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000315",
       "meta" : {
         "definition" : {
-          "val" : "Region of sequence similarity by descent from a common ancestor.",
+          "val" : "The first base where RNA polymerase begins to synthesize the RNA transcript.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Conserved_region"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:conserved_region",
+          "val" : "transcription_start_site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "transcription start site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasBroadSynonym",
@@ -41809,7 +46225,7 @@
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conserved region",
+          "val" : "INSDC_note:transcription_start_site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -41818,17 +46234,25 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conserved_region"
+      "lbl" : "TSS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001661",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001649",
       "meta" : {
         "definition" : {
-          "val" : "A TATA box core promoter of a gene transcribed by RNA polymerase II.",
-          "xrefs" : [ "PMID:16858867" ]
+          "val" : "A repeat that is disrupted by the insertion of another element.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "RNA polymerase II TATA box",
+          "val" : "nested repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:nested",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -41836,79 +46260,90 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T02:42:12Z"
+          "val" : "2010-06-23T03:24:55Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_polymerase_II_TATA_box"
+      "lbl" : "nested_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001660",
+      "id" : "http://purl.obolibrary.org/obo/BS_00337",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001070"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000318",
       "meta" : {
+        "definition" : {
+          "val" : "First codon to be translated by a ribosome.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Start_codon"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "core promoter element",
+          "val" : "start codon",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "general transcription factor binding site",
+          "pred" : "hasExactSynonym",
+          "val" : "initiation codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T11:49:03Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "core_promoter_element"
+      "lbl" : "start_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001663",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001648",
       "meta" : {
         "definition" : {
-          "val" : "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).",
-          "xrefs" : [ "PMID:16858867" ]
+          "val" : "A transposon that is disrupted by the insertion of another element.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "BREd motif",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "BREd",
+          "val" : "nested transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T02:49:55Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2010-06-23T03:22:57Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "BREd_motif"
+      "lbl" : "nested_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000332",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000317",
       "meta" : {
         "definition" : {
-          "val" : "Coding region of sequence similarity by descent from a common ancestor.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.",
+          "xrefs" : [ "http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "coding conserved region",
+          "val" : "cDNA clone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -41917,22 +46352,31 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_conserved_region"
+      "lbl" : "cDNA_clone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000331",
+      "id" : "http://purl.obolibrary.org/obo/BS_00336",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001146"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000796",
       "meta" : {
         "definition" : {
-          "val" : "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.",
-          "xrefs" : [ "http://www.biospace.com" ]
+          "val" : "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE.",
+          "xrefs" : [ "FB:mc" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Modified as requested by Lynn - FB. May 2007." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:STS",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence tag site",
+          "val" : "transgenic transposable element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -41941,82 +46385,118 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "STS"
+      "lbl" : "transgenic_transposable_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001662",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000312",
       "meta" : {
         "definition" : {
-          "val" : "A TATA box core promoter of a gene transcribed by RNA polymerase III.",
+          "val" : "Attribute to describe a feature that has been experimentally verified.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA polymerase III TATA box",
+          "val" : "experimentally determined",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T02:43:16Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_polymerase_III_TATA_box"
+      "lbl" : "experimentally_determined"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001658",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001643",
       "meta" : {
         "definition" : {
-          "val" : "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.",
-          "xrefs" : [ "SO:AF" ]
+          "val" : "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http:http://en.wikipedia.org/wiki/Telomerase_RNA_component"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "NTR",
+          "val" : "TERC",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nested tandem repeat",
+          "val" : "telomerase RNA gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Telomerase RNA component",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-05-18T05:26:38Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "telomerase_RNA_gene"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001642",
+      "meta" : {
+        "definition" : {
+          "val" : "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness.",
+          "xrefs" : [ "SO:jestill" ]
+        },
+        "comments" : [ "Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "mathematically defined repeat",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-08-26T09:36:16Z"
+          "val" : "2010-05-03T11:50:14Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Tracker ID: 3052459."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nested_tandem_repeat"
+      "lbl" : "mathematically_defined_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000327",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000311",
       "meta" : {
         "definition" : {
-          "val" : "The last base to be translated into protein. It does not include the stop codon.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : ".",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "similar to:<sequence_id>" ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "computed_feature_by_similarity"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000795",
+      "meta" : {
+        "definition" : {
+          "val" : "A mini_gene that rescues.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translation_end",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "coding end",
+          "val" : "rescue mini gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "translation termination site",
+          "val" : "rescue mini-gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42025,43 +46505,48 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_end"
+      "lbl" : "rescue_mini_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001657",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000314",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.",
+          "val" : "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Direct_repeat"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ligand binding site",
+          "val" : "direct repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:direct",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-08-03T12:32:58Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ligand_binding_site"
+      "lbl" : "direct_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000326",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000798",
       "meta" : {
         "definition" : {
-          "val" : "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract" ]
+          "val" : "TE that has been modified by manipulations in vitro.",
+          "xrefs" : [ "FB:mc" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SAGE tag",
+          "val" : "engineered transposable element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42070,84 +46555,104 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SAGE_tag"
+      "lbl" : "engineered_transposable_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000329",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001645",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA with a plus 2 frameshift.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A measurable sequence feature that varies within a population.",
+          "xrefs" : [ "SO:db" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mRNA with plus 2 frameshift",
+          "pred" : "hasRelatedSynonym",
+          "val" : "genetic marker",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-05-28T02:33:07Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_with_plus_2_frameshift"
+      "lbl" : "genetic_marker"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001659",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001644",
       "meta" : {
+        "definition" : {
+          "val" : "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications.",
+          "xrefs" : [ "MGD:tm", "PMID:10354467" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "promoter element",
+          "pred" : "hasRelatedSynonym",
+          "val" : "targeting vector",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-01T11:48:32Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-05-28T02:05:25Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "promoter_element"
+      "lbl" : "targeting_vector"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000328",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000313",
       "meta" : {
+        "definition" : {
+          "val" : "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Stem_loop"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "microarray oligo",
+          "val" : "RNA_hairpin_loop",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "microarray oligonucleotide",
+          "val" : "INSDC_feature:stem_loop",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stem-loop",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stem loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0000019"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "microarray_oligo"
+      "lbl" : "stem_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000323",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000797",
       "meta" : {
         "definition" : {
-          "val" : "The first base to be translated into protein.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "TE that exists (or existed) in nature.",
+          "xrefs" : [ "FB:mc" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "translation start",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "coding start",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "translation initiation site",
+          "val" : "natural transposable element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42156,247 +46661,207 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_start"
+      "lbl" : "natural_transposable_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001654",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000792",
       "meta" : {
-        "definition" : {
-          "val" : "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "nucleotide to protein binding site",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "cloned_cDNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000791",
+      "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-08-03T12:26:05Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "nucleotide_to_protein_binding_site"
+      "lbl" : "cloned_genomic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001653",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000794",
       "meta" : {
         "definition" : {
-          "val" : "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.",
-          "xrefs" : [ "PMID:11327309", "PMID:19917671" ]
+          "val" : "A rescue region that is engineered.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "retinoic acid responsive element",
+          "val" : "engineered rescue fragment",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "RARE",
+          "val" : "engineered rescue segment",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "engineered rescue region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-08-03T10:46:12Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "retinoic_acid_responsive_element"
+      "lbl" : "engineered_rescue_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000322",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000310",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "nuclease hypersensitive site",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "nuclease_hypersensitive_site"
+      "lbl" : "predicted_ab_initio_computation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000325",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001641",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a large ribosomal subunit RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that encodes a long, intervening non-coding RNA.",
+          "xrefs" : [ "PMID:23463798", "SO:ke", "http://www.gencodegenes.org/gencode_biotypes.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "35S rRNA primary transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "rRNA large subunit primary transcript",
+          "val" : "lincRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-21T10:14:24Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_large_subunit_primary_transcript"
+      "lbl" : "lincRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001656",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001640",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A gene that encodes a RNase_MRP_RNA.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "metal binding site",
+          "val" : "RNase MRP RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-21T10:13:58Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-08-03T12:31:42Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "See GO:0046872 : metal ion binding."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "metal_binding_site"
+      "lbl" : "RNase_MRP_RNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#genome_of",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000793",
       "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
-      "type" : "PROPERTY",
-      "lbl" : "genome_of"
+      "type" : "CLASS",
+      "lbl" : "engineered_DNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000324",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000790",
       "meta" : {
         "definition" : {
-          "val" : "A nucleotide sequence that may be used to identify a larger sequence.",
+          "val" : "An attribute describing a feature that is invalidated.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tag"
+      "lbl" : "invalidated"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001655",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000309",
       "meta" : {
-        "definition" : {
-          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.",
-          "xrefs" : [ "SO:cb" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "np_bind",
-          "xrefs" : [ "uniprot:feature" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nucleotide binding site",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "See GO:0000166 : nucleotide binding."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-08-03T12:30:04Z"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "nucleotide_binding_site"
+      "lbl" : "computed_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001694",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001639",
       "meta" : {
         "definition" : {
-          "val" : "A restriction enzyme cleavage site whereby only one strand is cut.",
+          "val" : "A gene that encodes an RNase P RNA.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Moved under enzymatic_RNA_gene on 18 Nov 2021. See GitHub Issue #533." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "single strand restriction enzyme cleavage site",
+          "pred" : "hasExactSynonym",
+          "val" : "RNase P RNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:44:48Z"
+          "val" : "2010-04-21T10:13:23Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "single_strand_restriction_enzyme_cleavage_site"
+      "lbl" : "RNase_P_RNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000363",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000308",
       "meta" : {
-        "definition" : {
-          "val" : "A transgene that is floxed.",
-          "xrefs" : [ "SO:xp" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "floxed gene",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "floxed_gene"
+      "lbl" : "sequence_feature_locating_method"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001210",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000305",
       "meta" : {
         "definition" : {
-          "val" : "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A modified nucleotide, i.e. a nucleotide other than A, T, C. G.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Translational_frameshift"
-        } ],
+        "comments" : [ "Modified base:<modified_base>." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translational frameshift",
+          "val" : "modified base site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ribosomal frameshift",
+          "val" : "INSDC_feature:modified_base",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42405,108 +46870,135 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translational_frameshift"
+      "lbl" : "modified_DNA_base"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001693",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001636",
       "meta" : {
         "definition" : {
-          "val" : "A restriction enzyme cleavage site where both strands are cut at the same position.",
+          "val" : "A sequence variant located within 2KB 5' of a gene.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "blunt end restriction enzyme cleavage site",
+          "pred" : "hasExactSynonym",
+          "val" : "near-gene-5",
+          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbsnp"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "2KB upstream variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:43:14Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-24T09:51:22Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "blunt_end_restriction_enzyme_cleavage_junction"
+      "lbl" : "2KB_upstream_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000362",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000789",
       "meta" : {
         "definition" : {
-          "val" : "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "An attribute to describe a feature that has been proven.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "invalidated by chimeric cDNA",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "invalidated_by_chimeric_cDNA"
+      "lbl" : "validated"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001696",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001635",
       "meta" : {
         "definition" : {
-          "val" : "A region that has been implicated in binding although the exact coordinates of binding may be unknown.",
+          "val" : "A sequence variant located within 5KB 5' of a gene.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript." ],
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "experimentally defined binding region",
+          "pred" : "hasExactSynonym",
+          "val" : "5kb upstream variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "upstream",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:upstream-gene",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-11-02T11:39:59Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2010-03-24T09:51:06Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "experimentally_defined_binding_region"
+      "lbl" : "5KB_upstream_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001212",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000304",
       "meta" : {
         "definition" : {
-          "val" : "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site.",
+          "xrefs" : [ "http://www.promega.com" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "plus 2 ribosomal frameshift",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "plus 2 translational frameshift",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "type_II_enzyme_restriction_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000788",
+      "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "plus_2_translational_frameshift"
+      "lbl" : "cloned"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000365",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000307",
       "meta" : {
         "definition" : {
-          "val" : "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.",
-          "xrefs" : [ "SO:as" ]
+          "val" : "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes.",
+          "xrefs" : [ "SO:rd" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Integron"
+          "val" : "http://en.wikipedia.org/wiki/CpG_island"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "CpG island",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CG island",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -42514,21 +47006,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "integron"
+      "lbl" : "CpG_island"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001695",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001638",
       "meta" : {
         "definition" : {
-          "val" : "A terminal region of DNA sequence where the end of the region is not blunt ended.",
+          "val" : "A gene that encodes for an piwi associated RNA.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Moved from ncRNA_gene to sncRNA_gene 27 April 2021 to be more consistent with the organization of the ncRNA branch of SO. Requested by FlyBase, moved by Dave Sant. See GitHub Issue #514." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sticky end",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "single strand overhang",
+          "val" : "piRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42536,47 +47025,55 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:48:35Z"
+          "val" : "2010-04-21T10:11:36Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_single_strand_overhang"
+      "lbl" : "piRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001211",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001637",
       "meta" : {
         "definition" : {
-          "val" : "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
+          "val" : "A gene that encodes for ribosomal RNA.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Adjusted heirarchy and names of rRNA_gene terms at the request of Steven Marygold GitHub Issue #513 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/513)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plus 1 translational frameshift",
+          "val" : "rDNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "plus 1 ribosomal frameshift",
+          "val" : "rRNA gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-21T10:10:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plus_1_translational_frameshift"
+      "lbl" : "rRNA_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000364",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000306",
       "meta" : {
         "definition" : {
-          "val" : "The region of sequence surrounding a transposable element.",
+          "val" : "A nucleotide modified by methylation.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transposable element flanking region",
+          "val" : "methylated base feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42585,38 +47082,68 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transposable_element_flanking_region"
+      "lbl" : "methylated_DNA_base_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001690",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001632",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant located 3' of a gene.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3' restriction enzyme junction",
+          "val" : "snpEff:DOWNSTREAM",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:downstream_gene_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:downstream",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "downstream gene variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:downstream_gene_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:37:52Z"
+          "val" : "2010-03-24T09:49:38Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_restriction_enzyme_junction"
+      "lbl" : "downstream_gene_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000361",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000301",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A feature where recombination has occurred for the purpose of generating a diversity in the immune system.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "FRT flanked",
+          "val" : "vertebrate immune system gene recombination feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42625,43 +47152,76 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "FRT_flanked"
+      "lbl" : "vertebrate_immune_system_gene_recombination_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001692",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym",
+      "type" : "PROPERTY",
+      "lbl" : "has_narrow_synonym"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000785",
       "meta" : {
+        "definition" : {
+          "val" : "The region of sequence that has been inserted and is being propagated by the clone.",
+          "xrefs" : [ ]
+        },
+        "comments" : [ "Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sticky end restriction enzyme cleavage site",
+          "pred" : "hasExactSynonym",
+          "val" : "cloned segment",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cloned region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:40:50Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sticky_end_restriction_enzyme_cleavage_site"
+      "lbl" : "cloned_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001691",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001631",
       "meta" : {
         "definition" : {
-          "val" : "A restriction enzyme recognition site that, when cleaved, results in no overhangs.",
-          "xrefs" : [ "SBOL:jgquinn", "SO:ke" ]
+          "val" : "A sequence variant located 5' of a gene.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references." ],
+        "xrefs" : [ {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        }, {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "blunt end restriction enzyme cleavage site",
+          "val" : "upstream gene variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:upstream_gene_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:UPSTREAM",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:upstream",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:upstream_gene_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:39:53Z"
+          "val" : "2010-03-24T09:49:13Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -42671,17 +47231,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "blunt_end_restriction_enzyme_cleavage_site"
+      "lbl" : "upstream_gene_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000360",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000300",
       "meta" : {
         "definition" : {
-          "val" : "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A location where a gene is rearranged due to recombination during mitosis or meiosis.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Codon"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "recombination feature of rearranged gene",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -42689,76 +47250,108 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "codon"
+      "lbl" : "recombination_feature_of_rearranged_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001207",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000784",
       "meta" : {
         "definition" : {
-          "val" : "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.",
-          "xrefs" : [ "xenbase:jb" ]
+          "val" : "An attribute to describe a region from another species.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "foreign"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001634",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant located within a half KB of the end of a gene.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T7 RNA Polymerase Promoter",
+          "val" : "500B downstream variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "near-gene-3",
+          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbsnp"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-24T09:50:42Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "T7_RNA_Polymerase_Promoter"
+      "lbl" : "500B_downstream_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000359",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000303",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing sequence that is flanked by Lox-P sites.",
+          "val" : "Part of the primary transcript that is clipped off during processing.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Floxed"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "floxed"
+      "lbl" : "clip"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001206",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000787",
       "meta" : {
-        "definition" : {
-          "val" : "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.",
-          "xrefs" : [ "xenbase:jb" ]
-        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "clone_attribute"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000786",
+      "meta" : {
+        "comments" : [ "Added jan 2006 by KE." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "T3 RNA Polymerase Promoter",
+          "val" : "reagent attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "T3_RNA_Polymerase_Promoter"
+      "lbl" : "reagent_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001209",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000302",
       "meta" : {
         "definition" : {
-          "val" : "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/About/primer/est.html" ]
+          "val" : "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence.",
+          "xrefs" : [ "http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3' EST",
+          "val" : "J-RS",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "three prime EST",
+          "val" : "J gene recombination feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42767,40 +47360,72 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_EST"
+      "lbl" : "J_gene_recombination_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001208",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001633",
       "meta" : {
         "definition" : {
-          "val" : "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/About/primer/est.html" ]
+          "val" : "A sequence variant located within 5 KB of the end of a gene.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript." ],
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "5' EST",
+          "pred" : "hasRelatedSynonym",
+          "val" : "within 5KB downstream",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five prime EST",
+          "val" : "Seattleseq:downstream-gene",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5KB downstream variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "downstream",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-24T09:50:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_EST"
+      "lbl" : "5KB_downstream_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001203",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000341",
       "meta" : {
         "definition" : {
-          "val" : "A region (DNA) to which RNA polymerase binds, to begin transcription.",
-          "xrefs" : [ "xenbase:jb" ]
+          "val" : "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Cytological_band"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA polymerase promoter",
+          "val" : "cytoband",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "chromosome band",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytological band",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42809,21 +47434,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_polymerase_promoter"
+      "lbl" : "chromosome_band"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001687",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001672",
       "meta" : {
         "definition" : {
-          "val" : "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A DNA sequence to which bacterial RNA polymerase sigma 54 binds, to begin transcription.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "restriction enzyme recognition site",
+          "val" : "bacterial RNA polymerase promoter sigma54",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "restriction endonuclease recognition site",
+          "pred" : "hasRelatedSynonym",
+          "val" : "<new synonym>",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42831,102 +47456,108 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:29:57Z"
+          "val" : "2010-10-06T01:42:37Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_recognition_site"
+      "lbl" : "bacterial_RNApol_promoter_sigma54_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000356",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001671",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A DNA sequence to which bacterial RNA polymerase sigma 70 binds, to begin transcription.",
+          "xrefs" : [ ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "bacterial RNA polymerase promoter sigma 70",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-06T01:41:34Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA"
+      "lbl" : "bacterial_RNApol_promoter_sigma_70_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000100",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000340",
       "meta" : {
         "definition" : {
-          "val" : ".",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation causing polypeptide N terminal elongation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "polypeptide N-terminal elongation",
-          "xrefs" : [ ]
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Chromosome"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001611"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutation_causing_polypeptide_N_terminal_elongation"
+      "lbl" : "chromosome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001686",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000343",
       "meta" : {
         "definition" : {
-          "val" : "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.",
+          "val" : "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "match"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001674",
+      "meta" : {
+        "definition" : {
+          "val" : "A conserved region about 24-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.",
+          "xrefs" : [ "PMID:18331472" ]
+        },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "quality value",
+          "val" : "minus 24 signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-28T02:24:11Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-06T01:45:24Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "quality_value"
+      "lbl" : "minus_24_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001202",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000342",
       "meta" : {
         "definition" : {
-          "val" : "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region specifically recognised by a recombinase where recombination can occur during mitosis or meiosis.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ambisense ssRNA viral sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ambisense single stranded RNA virus",
+          "val" : "site specific recombination target region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42935,61 +47566,67 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ambisense_ssRNA_viral_sequence"
+      "lbl" : "site_specific_recombination_target_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000355",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001673",
       "meta" : {
         "definition" : {
-          "val" : "A region of the genome which is co-inherited as the result of the lack of historic recombination within it.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54.",
+          "xrefs" : [ "PMID:18331472" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "haplotype block",
+          "val" : "minus 12 signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-06T01:44:57Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "haplotype_block"
+      "lbl" : "minus_12_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001689",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001670",
       "meta" : {
         "definition" : {
-          "val" : "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A regulatory promoter element that is distal from the TSS.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "5' restriction enzyme junction",
+          "pred" : "hasRelatedSynonym",
+          "val" : "distal promoter element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:36:24Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T03:21:08Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_restriction_enzyme_junction"
+      "lbl" : "distal_promoter_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001205",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000338",
       "meta" : {
         "definition" : {
-          "val" : "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.",
-          "xrefs" : [ "xenbase:jb" ]
+          "val" : "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins.",
+          "xrefs" : [ "http://www.pnas.org/cgi/content/full/97/18/10083" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SP6 RNA Polymerase Promoter",
+          "val" : "miniature inverted repeat transposable element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -42998,17 +47635,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SP6_RNA_Polymerase_Promoter"
+      "lbl" : "MITE"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001688",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001669",
       "meta" : {
         "definition" : {
-          "val" : "The boundary at which a restriction enzyme breaks the nucleotide sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.",
+          "xrefs" : [ "PMID:16858867" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "restriction enzyme cleavage junction",
+          "val" : "RNApol II core promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43019,35 +47656,51 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-29T12:35:02Z"
+          "val" : "2010-10-01T03:13:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_cleavage_junction"
+      "lbl" : "RNApol_II_core_promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000357",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001668",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a region that is bounded either side by a particular kind of region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor).",
+          "xrefs" : [ "PMID:12515390", "PMID:9679020", "SO:ml" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "specific transcription factor binding site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "proximal promoter element",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T03:10:23Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "flanked"
+      "lbl" : "proximal_promoter_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001204",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000337",
       "meta" : {
         "definition" : {
-          "val" : "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.",
-          "xrefs" : [ "xenbase:jb" ]
+          "val" : "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference.",
+          "xrefs" : [ "SO:rd" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Phage RNA Polymerase Promoter",
+          "val" : "RNAi reagent",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43056,112 +47709,76 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Phage_RNA_Polymerase_Promoter"
+      "lbl" : "RNAi_reagent"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001683",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000339",
       "meta" : {
         "definition" : {
-          "val" : "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.",
-          "xrefs" : [ "http://en.wikipedia.org/wiki/Sequence_motif" ]
+          "val" : "A region in a genome which promotes recombination.",
+          "xrefs" : [ "SO:rd" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Sequence_motif"
+          "val" : "http://en.wikipedia.org/wiki/Recombination_hotspot"
         } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "sequence motif",
+          "pred" : "hasExactSynonym",
+          "val" : "recombination hotspot",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T04:13:22Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "sequence_motif"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000352",
-      "meta" : {
-        "definition" : {
-          "val" : "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.",
-          "xrefs" : [ "RSC:cb" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DNA"
+      "lbl" : "recombination_hotspot"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001682",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000334",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region that is involved in the control of the process of nucleotide replication.",
+          "val" : "Non-coding region of sequence similarity by descent from a common ancestor.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:replication_regulatory_region",
+          "val" : "conserved non-coding element",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "pred" : "hasExactSynonym",
+          "val" : "nc conserved region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "replication regulatory region",
+          "val" : "conserved non-coding sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "noncoding conserved region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-12T03:54:09Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "replication_regulatory_region"
+      "lbl" : "nc_conserved_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000351",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001665",
       "meta" : {
         "definition" : {
-          "val" : "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.",
-          "xrefs" : [ "SO:ma" ]
-        },
+          "val" : "A sub element of the DCE core promoter element, with consensus sequence CTTC.",
+          "xrefs" : [ "PMID:16858867", "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "synthetic sequence",
+          "pred" : "hasRelatedSynonym",
+          "val" : "DCE SI",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "synthetic_sequence"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001685",
-      "meta" : {
-        "definition" : {
-          "val" : "The score of an experimentally derived feature such as a p-value.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-28T02:23:16Z"
+          "val" : "2010-10-01T03:00:10Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -43171,40 +47788,43 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "score"
+      "lbl" : "DCE_SI"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000354",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001664",
       "meta" : {
         "definition" : {
-          "val" : "A region of intronic nucleotide sequence targeted by a nuclease enzyme.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII.",
+          "xrefs" : [ "PMID:16858867" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "group 1 intron homing endonuclease target region",
+          "pred" : "hasRelatedSynonym",
+          "val" : "downstream core element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T02:56:41Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "group_1_intron_homing_endonuclease_target_region"
+      "lbl" : "DCE"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001201",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000333",
       "meta" : {
         "definition" : {
-          "val" : "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.",
+          "val" : "The boundary between two exons in a processed transcript.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "positive sense single stranded RNA virus",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "positive sense ssRNA viral sequence",
+          "val" : "exon junction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43213,21 +47833,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "positive_sense_ssRNA_viral_sequence"
+      "lbl" : "exon_junction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000353",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000336",
       "meta" : {
         "definition" : {
-          "val" : "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog).",
+          "xrefs" : [ "http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#Alliance_of_Genome_Resources" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Sequence_assembly"
+          "val" : "http://en.wikipedia.org/wiki/Pseudogene"
         } ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:gene",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence assembly",
+          "val" : "INSDC_qualifier:pseudo",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:unknown",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43236,46 +47864,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_assembly"
+      "lbl" : "pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001684",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001667",
       "meta" : {
         "definition" : {
-          "val" : "An attribute of an experimentally derived feature.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sub element of the DCE core promoter element with consensus sequence AGC.",
+          "xrefs" : [ "PMID:16858867", "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "experimental feature attribute",
+          "pred" : "hasExactSynonym",
+          "val" : "DCE SIII",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T03:00:44Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-28T02:22:23Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "experimental_feature_attribute"
+      "lbl" : "DCE_SIII"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001200",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000335",
       "meta" : {
         "definition" : {
-          "val" : "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.",
+          "val" : "A mRNA with a minus 2 frameshift.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "negative sense ssRNA viral sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "negative sense single stranded RNA virus",
+          "val" : "mRNA with minus 2 frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43284,139 +47908,157 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "negative_sense_ssRNA_viral_sequence"
+      "lbl" : "mRNA_with_minus_2_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000350",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001666",
       "meta" : {
         "definition" : {
-          "val" : "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A sub element of the DCE core promoter element with consensus sequence CTGT.",
+          "xrefs" : [ "PMID:16858867", "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "FLP recombination target region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "FRT site",
+          "val" : "DCE SII",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T03:00:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "FRT_site"
+      "lbl" : "DCE_SII"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001681",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000330",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region that is involved in the control of the process of recombination.",
+          "val" : "Region of sequence similarity by descent from a common ancestor.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Conserved_region"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "recombination regulatory region",
+          "val" : "conserved region",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-12T03:53:35Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_feature",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_note:conserved_region",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombination_regulatory_region"
+      "lbl" : "conserved_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001680",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001661",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region that is involved in the control of the process of translation.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A TATA box core promoter of a gene transcribed by RNA polymerase II.",
+          "xrefs" : [ "PMID:16858867" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translation regulatory region",
+          "val" : "RNA polymerase II TATA box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T02:42:12Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-12T03:52:45Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translation_regulatory_region"
+      "lbl" : "RNA_polymerase_II_TATA_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000349",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001660",
       "meta" : {
         "definition" : {
-          "val" : "A match against a protein sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An element that only exists within the promoter region of a eukaryotic gene.",
+          "xrefs" : [ "GREEKC:cl" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "general transcription factor binding site",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "protein match",
+          "val" : "core eukaryotic promoter element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T11:49:03Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "protein_match"
+      "lbl" : "core_eukaryotic_promoter_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001679",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001663",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region that is involved in the control of the process of transcription.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A core RNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G).",
+          "xrefs" : [ "PMID:16858867" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcription regulatory region",
+          "val" : "BREd",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "BREd motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-12T03:49:35Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T02:49:55Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcription_regulatory_region"
+      "lbl" : "BREd_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000348",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000332",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.",
-          "xrefs" : [ "CHEBI:33696", "RSC:cb" ]
+          "val" : "Coding region of sequence similarity by descent from a common ancestor.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Nucleic_acid"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nucleic acid",
+          "val" : "coding conserved region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43425,120 +48067,124 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nucleic_acid"
+      "lbl" : "coding_conserved_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001676",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001662",
       "meta" : {
         "definition" : {
-          "val" : "An A box within an RNA polymerase III type 2 promoter.",
+          "val" : "A TATA box core promoter of a gene transcribed by RNA polymerase III.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "A box type 2",
+          "pred" : "hasExactSynonym",
+          "val" : "RNA polymerase III TATA box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-06T05:44:18Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-01T02:43:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "A_box_type_2"
+      "lbl" : "RNA_polymerase_III_TATA_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000345",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000331",
       "meta" : {
         "definition" : {
-          "val" : "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known.",
+          "xrefs" : [ "http://www.biospace.com" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "expressed sequence tag",
+          "val" : "INSDC_feature:STS",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence tag site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "EST"
+      "lbl" : "STS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#maximally_overlaps",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000327",
       "meta" : {
         "definition" : {
-          "val" : "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.",
-          "xrefs" : [ "PMID:20226267" ]
+          "val" : "The last base to be translated into protein. It does not include the stop codon.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-14T01:34:48Z"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "coding end",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR."
+          "pred" : "hasExactSynonym",
+          "val" : "translation termination site",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "translation_end",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "maximally_overlaps"
+      "type" : "CLASS",
+      "lbl" : "coding_end"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001675",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001658",
       "meta" : {
         "definition" : {
-          "val" : "An A box within an RNA polymerase III type 1 promoter.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other.",
+          "xrefs" : [ "SO:AF" ]
         },
+        "comments" : [ "Tracker ID: 3052459." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "A box type 1",
+          "pred" : "hasExactSynonym",
+          "val" : "NTR",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "nested tandem repeat",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-06T05:43:43Z"
+          "val" : "2010-08-26T09:36:16Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "A_box_type_1"
+      "lbl" : "nested_tandem_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000344",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000326",
       "meta" : {
         "definition" : {
-          "val" : "Region of a transcript that regulates splicing.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice enhancer",
+          "val" : "SAGE tag",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43547,17 +48193,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_enhancer"
+      "lbl" : "SAGE_tag"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001678",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001657",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.",
-          "xrefs" : [ "PMID:12381659" ]
+          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "regulatory promoter element",
+          "pred" : "hasExactSynonym",
+          "val" : "ligand binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43568,22 +48214,21 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-07T04:39:48Z"
+          "val" : "2010-08-03T12:32:58Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regulatory_promoter_element"
+      "lbl" : "ligand_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000347",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000329",
       "meta" : {
         "definition" : {
-          "val" : "A match against a nucleotide sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An mRNA with a plus 2 frameshift.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nucleotide match",
+          "val" : "mRNA with plus 2 frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43592,17 +48237,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nucleotide_match"
+      "lbl" : "mRNA_with_plus_2_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000346",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000328",
       "meta" : {
+        "definition" : {
+          "val" : "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Cre-recombination target region",
+          "pred" : "hasExactSynonym",
+          "val" : "microarray oligo",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "loxP site",
+          "val" : "microarray oligonucleotide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43611,21 +48260,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "loxP_site"
+      "lbl" : "microarray_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001677",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001659",
       "meta" : {
         "definition" : {
-          "val" : "A core promoter region of RNA polymerase III type 1 promoters.",
-          "xrefs" : [ "PMID:12381659" ]
+          "val" : "An element that can exist within the promoter region of a gene.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "IE",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "intermediate element",
+          "val" : "promoter element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43636,30 +48282,29 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-10-06T05:52:03Z"
+          "val" : "2010-10-01T11:48:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intermediate_element"
+      "lbl" : "promoter_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000385",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000323",
       "meta" : {
         "definition" : {
-          "val" : "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030" ]
+          "val" : "The first base to be translated into protein.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:RNase_MRP_RNA",
+          "val" : "coding start",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RNase MRP RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "translation start",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "translation initiation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43668,65 +48313,44 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNase_MRP_RNA"
+      "lbl" : "coding_start"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001232",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001654",
       "meta" : {
         "definition" : {
-          "val" : "A modified RNA base in which thymine is bound to the ribose ring.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The free molecule is CHEBI:30832."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "ribothymidine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000115",
-      "meta" : {
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing complex 3D structural change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing complex 3D structural change",
+          "val" : "nucleotide to protein binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-08-03T12:26:05Z"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001600"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_complex_3D_structural_change"
+      "lbl" : "nucleotide_to_protein_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000384",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000322",
       "meta" : {
         "definition" : {
-          "val" : "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035" ]
+          "val" : "A region of nucleotide sequence targeted by a nuclease enzyme that is found cleaved more than would be expected by chance.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/OxyS_RNA"
-        } ],
+        "comments" : [ "Relationship to accessible_DNA_region added 11 Feb 2021. GREEKC pointed out that this is an assay based term, but we need a biological term for the accessible DNA. See GitHub Issue #531." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "OxyS RNA",
+          "val" : "nuclease hypersensitive site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43735,64 +48359,78 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "OxyS_RNA"
+      "lbl" : "nuclease_hypersensitive_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001231",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001653",
       "meta" : {
         "definition" : {
-          "val" : "A modified RNA base in which guanine is methylated at the 7- position.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind.",
+          "xrefs" : [ "PMID:11327309", "PMID:19917671" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "seven methylguanine",
+          "val" : "retinoic acid responsive element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "7-methylguanine",
+          "val" : "RARE",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-08-03T10:46:12Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The free molecule is CHEBI:2274."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "seven_methylguanine"
+      "lbl" : "retinoic_acid_responsive_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000387",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001656",
       "meta" : {
         "definition" : {
-          "val" : "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034" ]
+          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions.",
+          "xrefs" : [ "SO:cb" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/RprA_RNA"
-        } ],
+        "comments" : [ "See GO:0046872 : metal ion binding." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "RprA RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "metal binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-08-03T12:31:42Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RprA_RNA"
+      "lbl" : "metal_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001234",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000325",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a feature that has either intra-genome or intracellular mobility.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A primary transcript encoding a large ribosomal subunit RNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Mobile"
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "35S rRNA primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "rRNA large subunit primary transcript",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -43800,108 +48438,98 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mobile"
+      "lbl" : "rRNA_large_subunit_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000112",
+      "id" : "http://purl.obolibrary.org/obo/so#genome_of",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing no 3D structural change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing no 3D structural change",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term."
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_no_3D_structural_change"
+      "type" : "PROPERTY",
+      "lbl" : "genome_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000386",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000324",
       "meta" : {
         "definition" : {
-          "val" : "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010" ]
+          "val" : "A nucleotide sequence that may be used to identify a larger sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:RNase_P_RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RNase P RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNase_P_RNA"
+      "lbl" : "tag"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001233",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001655",
       "meta" : {
         "definition" : {
-          "val" : "A modified RNA base in which methylhypoxanthine is bound to the ribose ring.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues.",
+          "xrefs" : [ "SO:cb" ]
         },
+        "comments" : [ "See GO:0000166 : nucleotide binding." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "np_bind",
+          "xrefs" : [ "uniprot:feature" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "nucleotide binding site",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-08-03T12:30:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "methylinosine"
+      "lbl" : "nucleotide_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000119",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001694",
       "meta" : {
+        "definition" : {
+          "val" : "A restriction enzyme cleavage site whereby only one strand is cut.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing inactive ligand binding site",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing inactive ligand binding site",
+          "val" : "single strand restriction enzyme cleavage site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001560"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:44:48Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_inactive_ligand_binding_site"
+      "lbl" : "single_strand_restriction_enzyme_cleavage_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000381",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000363",
       "meta" : {
+        "definition" : {
+          "val" : "A transgene that is floxed.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "group IIA intron",
+          "val" : "floxed gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43910,29 +48538,33 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "group_IIA_intron"
+      "lbl" : "floxed_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000380",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001210",
       "meta" : {
         "definition" : {
-          "val" : "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.",
-          "xrefs" : [ "PMID:2436805" ]
+          "val" : "The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
+          "xrefs" : [ "SO:ke", "http://www.insdc.org/files/feature_table.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Added synonym 'ribosomal_slippage' on Feb 1, 2021, a term in INSDC and GenBank. See GitHub Issue #522." ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Hammerhead_ribozyme"
+          "val" : "http://en.wikipedia.org/wiki/Translational_frameshift"
         } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:ribosomal_slippage",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:hammerhead_ribozyme",
+          "val" : "ribosomal slippage",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "hammerhead ribozyme",
+          "val" : "translational frameshift",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ribosomal frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43941,52 +48573,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "hammerhead_ribozyme"
+      "lbl" : "translational_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000118",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001693",
       "meta" : {
+        "definition" : {
+          "val" : "A restriction enzyme cleavage site where both strands are cut at the same position.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing loss of function of polypeptide",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "loss of function of polypeptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing loss of function of polypeptide",
+          "val" : "blunt end restriction enzyme cleavage site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:43:14Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001559"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_loss_of_function_of_polypeptide"
+      "lbl" : "blunt_end_restriction_enzyme_cleavage_junction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000383",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000362",
       "meta" : {
         "definition" : {
-          "val" : "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033" ]
+          "val" : "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/MicF_RNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "MicF RNA",
+          "val" : "invalidated by chimeric cDNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -43995,149 +48617,134 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "MicF_RNA"
+      "lbl" : "invalidated_by_chimeric_cDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001230",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001696",
       "meta" : {
         "definition" : {
-          "val" : "A modified RNA base in which hypoxanthine is bound to the ribose ring.",
-          "xrefs" : [ "RSC:cb", "http://library.med.utah.edu/RNAmods/" ]
+          "val" : "A region that has been implicated in binding although the exact coordinates of binding may be unknown.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Inosine"
-        } ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "I",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "RNAMOD:017",
+          "val" : "experimentally defined binding region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The free molecule is CHEBI:17596."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-11-02T11:39:59Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inosine"
+      "lbl" : "experimentally_defined_binding_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000117",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001212",
       "meta" : {
+        "definition" : {
+          "val" : "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting polypeptide function",
+          "pred" : "hasExactSynonym",
+          "val" : "plus 2 ribosomal frameshift",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting polypeptide function",
+          "val" : "plus 2 translational frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001554"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_polypeptide_function"
+      "lbl" : "plus_2_translational_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000116",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000365",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing conformational change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing conformational change",
-          "xrefs" : [ ]
+        "definition" : {
+          "val" : "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site.",
+          "xrefs" : [ "SO:as" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Integron"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001601"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_conformational_change"
+      "lbl" : "integron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000382",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001695",
       "meta" : {
+        "definition" : {
+          "val" : "A terminal region of DNA sequence where the end of the region is not blunt ended.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "group IIB intron",
+          "val" : "single strand overhang",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "sticky end",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:48:35Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "group_IIB_intron"
+      "lbl" : "restriction_enzyme_single_strand_overhang"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001229",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000364",
       "meta" : {
         "definition" : {
-          "val" : "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "The region of sequence surrounding a transposable element.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:050"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Pseudouridine"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : " Y",
+          "val" : "transposable element flanking region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The free molecule is CHEBI:17802."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudouridine"
+      "lbl" : "transposable_element_flanking_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001228",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001211",
       "meta" : {
         "definition" : {
-          "val" : "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "RNAMOD:051"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Dihydrouridine"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : " D",
+          "val" : "plus 1 ribosomal frameshift",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "plus 1 translational frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44146,49 +48753,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dihydrouridine"
+      "lbl" : "plus_1_translational_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000122",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001690",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing polypeptide post translational processing change",
+        "definition" : {
+          "val" : "The restriction enzyme cleavage junction on the 3' strand of the nucleotide sequence.",
           "xrefs" : [ ]
-        }, {
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide post-translational processing affected",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing polypeptide post translational processing change",
+          "val" : "3' restriction enzyme junction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001562"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:37:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_polypeptide_post_translational_processing_change"
+      "lbl" : "three_prime_restriction_enzyme_junction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001225",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000361",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is silenced by histone modification.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene silenced by histone modification",
+          "val" : "FRT flanked",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44197,72 +48797,67 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_silenced_by_histone_modification"
+      "lbl" : "FRT_flanked"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000378",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001692",
       "meta" : {
         "definition" : {
-          "val" : "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014" ]
+          "val" : "A site where restriction enzymes can cleave that will produce an overhang or 'sticky end'.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/DsrA_RNA"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "DsrA RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "sticky end restriction enzyme cleavage site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:40:50Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DsrA_RNA"
+      "lbl" : "sticky_end_restriction_enzyme_cleavage_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000121",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001691",
       "meta" : {
+        "definition" : {
+          "val" : "A restriction enzyme recognition site that, when cleaved, results in no overhangs.",
+          "xrefs" : [ "SBOL:jgquinn", "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing polypeptide localization change",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing polypeptide localization change",
+          "val" : "blunt end restriction enzyme cleavage site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001558"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:39:53Z"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_polypeptide_localization_change"
+      "lbl" : "blunt_end_restriction_enzyme_cleavage_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000377",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000360",
       "meta" : {
         "definition" : {
-          "val" : "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018" ]
+          "val" : "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "CsrB RsmB RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "CsrB-RsmB RNA",
-          "xrefs" : [ ]
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Codon"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -44270,25 +48865,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CsrB_RsmB_RNA"
+      "lbl" : "codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001224",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001207",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is silenced by RNA interference.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription.",
+          "xrefs" : [ "xenbase:jb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA interference silenced gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RNAi silenced gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "gene silenced by RNA interference",
+          "val" : "T7 RNA Polymerase Promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44297,45 +48884,34 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_silenced_by_RNA_interference"
+      "lbl" : "T7_RNA_Polymerase_Promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000120",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000359",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing inactive catalytic site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing inactive catalytic site",
-          "xrefs" : [ ]
+        "definition" : {
+          "val" : "An attribute describing sequence that is flanked by Lox-P sites.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Floxed"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001618"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_inactive_catalytic_site"
+      "lbl" : "floxed"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001227",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001206",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is silenced by histone deacetylation.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription.",
+          "xrefs" : [ "xenbase:jb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene silenced by histone deacetylation",
+          "val" : "T3 RNA Polymerase Promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44344,20 +48920,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_silenced_by_histone_deacetylation"
+      "lbl" : "T3_RNA_Polymerase_Promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000379",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001209",
       "meta" : {
         "definition" : {
-          "val" : "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022" ]
+          "val" : "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs).",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/About/primer/est.html" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/GcvB_RNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "GcvB RNA",
+          "val" : "three prime EST",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3' EST",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44366,17 +48943,21 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "GcvB_RNA"
+      "lbl" : "three_prime_EST"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001226",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001208",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is silenced by histone methylation.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/About/primer/est.html" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene silenced by histone methylation",
+          "val" : "5' EST",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime EST",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44385,217 +48966,218 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_silenced_by_histone_methylation"
+      "lbl" : "five_prime_EST"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000374",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001687",
       "meta" : {
         "definition" : {
-          "val" : "An RNA with catalytic activity.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Ribozyme"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:ribozyme",
+          "val" : "restriction enzyme recognition site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasExactSynonym",
+          "val" : "restriction endonuclease recognition site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:29:57Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ribozyme"
+      "lbl" : "restriction_enzyme_recognition_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000104",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000100",
       "meta" : {
+        "definition" : {
+          "val" : ".",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutationt increasing level of translation product",
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide N-terminal elongation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant increasing level of translation product",
+          "val" : "mutation causing polypeptide N terminal elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001611"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_increasing_level_of_translation_product"
+      "lbl" : "mutation_causing_polypeptide_N_terminal_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001221",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001203",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an epigenetic process where a gene is inactivated by histone modification.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A region (DNA) to which RNA polymerase binds, to begin transcription.",
+          "xrefs" : [ "xenbase:jb" ]
         },
+        "comments" : [ "Term merged with promoter SO:0000167 in August 2020 as part of GREEKC initiative. See GitHub Issue 492 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/492)" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silenced by histone modification",
+          "val" : "RNA polymerase promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Histone modification is GO:0016570."
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0000167"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "silenced_by_histone_modification"
+      "lbl" : "RNA_polymerase_promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000373",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000356",
       "meta" : {
         "definition" : {
-          "val" : "A recombinationally rearranged gene by inversion.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "recombinationally inverted gene",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombinationally_inverted_gene"
+      "lbl" : "RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000103",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001686",
       "meta" : {
+        "definition" : {
+          "val" : "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant decreasing level of translation product",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "mutationdecreasing level of translation product",
+          "val" : "quality value",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001555"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "sequence_variant_decreasing_level_of_translation_product"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-28T02:24:11Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "quality_value"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001220",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001202",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an epigenetic process where a gene is inactivated by RNA interference.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silenced by RNA interference",
+          "val" : "ambisense ssRNA viral sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ambisense single stranded RNA virus",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "RNA interference is GO:0016246."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silenced_by_RNA_interference"
+      "lbl" : "ambisense_ssRNA_viral_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000102",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000355",
       "meta" : {
+        "definition" : {
+          "val" : "A region of the genome which is co-inherited as the result of the lack of historic recombination within it.",
+          "xrefs" : [ "SO:ma" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting level of translational product",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting level of translational product",
+          "val" : "haplotype block",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001553"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_level_of_translational_product"
+      "lbl" : "haplotype_block"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001223",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000358",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000104"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001689",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silenced by histone deacetylation",
+          "val" : "5' restriction enzyme junction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Histone deacetylation is GO:0016573."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:36:24Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silenced_by_histone_deacetylation"
+      "lbl" : "five_prime_restriction_enzyme_junction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000376",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001205",
       "meta" : {
         "definition" : {
-          "val" : "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013" ]
+          "val" : "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription.",
+          "xrefs" : [ "xenbase:jb" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/6S_RNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA 6S",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "6S RNA",
+          "val" : "SP6 RNA Polymerase Promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44604,230 +49186,195 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_6S"
+      "lbl" : "SP6_RNA_Polymerase_Promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000375",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000357",
       "meta" : {
         "definition" : {
-          "val" : "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002" ]
+          "val" : "An attribute describing a region that is bounded either side by a particular kind of region.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "5.8S rRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "rRNA 5 8S",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5.8S ribosomal RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5.8S LSU rRNA",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_5_8S"
+      "lbl" : "flanked"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000101",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001204",
       "meta" : {
         "definition" : {
-          "val" : ".",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.",
+          "xrefs" : [ "xenbase:jb" ]
         },
+        "comments" : [ "former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide C-terminal elongation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation causing polypeptide C terminal elongation",
+          "val" : "Phage RNA Polymerase Promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001610"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutation_causing_polypeptide_C_terminal_elongation"
+      "lbl" : "Phage_RNA_Polymerase_Promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001222",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001688",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing an epigenetic process where a gene is inactivated by histone methylation.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "The boundary at which a restriction enzyme breaks the nucleotide sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "silenced by histone methylation",
+          "val" : "restriction enzyme cleavage junction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-29T12:35:02Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Histone methylation is GO:0016571."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silenced_by_histone_methylation"
+      "lbl" : "restriction_enzyme_cleavage_junction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000108",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001683",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.",
+          "xrefs" : [ "http://en.wikipedia.org/wiki/Sequence_motif" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Sequence_motif"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mutaton causing inframe polypeptide C terminal elongation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "inframe_polypeptide C-terminal elongation",
+          "pred" : "hasRelatedSynonym",
+          "val" : "sequence motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001612"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T04:13:22Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutaton_causing_inframe_polypeptide_C_terminal_elongation"
+      "lbl" : "sequence_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000370",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000352",
       "meta" : {
         "definition" : {
-          "val" : "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others).",
-          "xrefs" : [ "PMID:28541282", "PomBase:al", "SO:ma" ]
+          "val" : "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "small regulatory ncRNA",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "small_regulatory_ncRNA"
+      "lbl" : "DNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000107",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000351",
       "meta" : {
+        "definition" : {
+          "val" : "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence.",
+          "xrefs" : [ "SO:ma" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "out of frame polypeptide N-terminal elongation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation causing out of frame polypeptide N terminal elongation",
+          "val" : "synthetic sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001615"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutation_causing_out_of_frame_polypeptide_N_terminal_elongation"
+      "lbl" : "synthetic_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000106",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001682",
       "meta" : {
+        "definition" : {
+          "val" : "A regulatory region that is involved in the control of the process of nucleotide replication.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mutation causing inframe polypeptide N terminal elongation",
+          "val" : "INSDC_qualifier:replication_regulatory_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "inframe polypeptide N-terminal elongation",
+          "val" : "replication regulatory region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001614"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-12T03:54:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutation_causing_inframe_polypeptide_N_terminal_elongation"
+      "lbl" : "replication_regulatory_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000372",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001685",
       "meta" : {
         "definition" : {
-          "val" : "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "The score of an experimentally derived feature such as a p-value.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "enzymatic RNA",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-28T02:23:16Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "enzymatic_RNA"
+      "lbl" : "score"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000371",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001201",
       "meta" : {
         "definition" : {
-          "val" : "A transposon that encodes function required for conjugation.",
-          "xrefs" : [ "http://www.sci.sdsu.edu/~smaloy/Glossary/C.html" ]
+          "val" : "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "positive sense single stranded RNA virus",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "conjugative transposon",
+          "val" : "positive sense ssRNA viral sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44836,88 +49383,88 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conjugative_transposon"
+      "lbl" : "positive_sense_ssRNA_viral_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000105",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000354",
       "meta" : {
+        "definition" : {
+          "val" : "A region of intronic nucleotide sequence targeted by a nuclease enzyme.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting polypeptide amino acid sequence",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting polypeptide amino acid sequence",
+          "val" : "group 1 intron homing endonuclease target region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001603"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_polypeptide_amino_acid_sequence"
+      "lbl" : "group_1_intron_homing_endonuclease_target_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000109",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000353",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Sequence_assembly"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "out of frame polypeptide C-terminal elongation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mutation causing out of frame polypeptide C terminal elongation",
+          "val" : "sequence assembly",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001613"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutation_causing_out_of_frame_polypeptide_C_terminal_elongation"
+      "lbl" : "sequence_assembly"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001218",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001684",
       "meta" : {
         "definition" : {
-          "val" : "An insertion that derives from another organism, via the use of recombinant DNA technology.",
-          "xrefs" : [ "SO:bm" ]
+          "val" : "An attribute of an experimentally derived feature.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "transgenic insertion",
+          "pred" : "hasRelatedSynonym",
+          "val" : "experimental feature attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-28T02:22:23Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transgenic_insertion"
+      "lbl" : "experimental_feature_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001217",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001200",
       "meta" : {
+        "definition" : {
+          "val" : "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "negative sense single stranded RNA virus",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "protein coding gene",
+          "val" : "negative sense ssRNA viral sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -44926,145 +49473,91 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "protein_coding_gene"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001219",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "retrogene"
+      "lbl" : "negative_sense_ssRNA_viral_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001214",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000350",
       "meta" : {
         "definition" : {
-          "val" : "The maximal intersection of exon and UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "noncoding region of exon",
+          "val" : "FRT site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "FLP recombination target region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "noncoding_region_of_exon"
+      "lbl" : "FRT_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000111",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001681",
       "meta" : {
         "definition" : {
-          "val" : "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule.",
+          "val" : "A regulatory region that is involved in the control of the process of recombination.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence_variant_causing_uncharacterised_3D_structural_change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting 3D-structure of polypeptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation affecting 3D structure of polypeptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing uncharacterised 3D structural change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing partially characterised 3D structural change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence variant affecting 3D structure of polypeptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence_variant_causing_partially_characterised_3D_structural_change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing uncharacterised 3D structural change",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mutation causing partially characterised 3D structural change",
+          "val" : "recombination regulatory region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001599"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000114"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000113"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-12T03:53:35Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_affecting_3D_structure_of_polypeptide"
+      "lbl" : "recombination_regulatory_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001698",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001680",
       "meta" : {
         "definition" : {
-          "val" : "\"A primer containing an SNV at the 3' end for accurate genotyping.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/11252801" ]
+          "val" : "A regulatory region that is involved in the control of the process of translation.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ASPE primer",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "allele specific primer extension primer",
+          "val" : "translation regulatory region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-11-11T03:25:21Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-12T03:52:45Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ASPE_primer"
+      "lbl" : "translation_regulatory_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000367",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000349",
       "meta" : {
         "definition" : {
-          "val" : "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.",
-          "xrefs" : [ "SO:as" ]
+          "val" : "A match against a protein sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "attI site",
+          "val" : "protein match",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -45073,236 +49566,230 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "attI_site"
+      "lbl" : "protein_match"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000366",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001679",
       "meta" : {
         "definition" : {
-          "val" : "The junction where an insertion occurred.",
+          "val" : "A regulatory region that is involved in the control of the process of transcription.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Obsoleted by David Sant on 11 Feb 2021 when it was merged with transcriptional_cis_regulatory_region (SO:0001055) to reduce redundancy and be consistent with Gene Ontology. See GitHub Issue #527." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insertion site",
+          "val" : "transcription regulatory region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-12T03:49:35Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "insertion_site"
+      "lbl" : "transcription_regulatory_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001697",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000348",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence identified by CHiP seq technology to contain a protein binding site.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone.",
+          "xrefs" : [ "CHEBI:33696", "RSC:cb" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Nucleic_acid"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ChIP seq region",
+          "pred" : "hasExactSynonym",
+          "val" : "nucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-11-02T11:43:07Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ChIP_seq_region"
+      "lbl" : "nucleic_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1000110",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001676",
       "meta" : {
         "definition" : {
-          "val" : "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame.",
+          "val" : "An A box within an RNA polymerase III type 2 promoter.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "frame restoring sequence variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "frame restoring mutation",
+          "pred" : "hasRelatedSynonym",
+          "val" : "A box type 2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-06T05:44:18Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "frame_restoring_sequence_variant"
+      "lbl" : "A_box_type_2"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001213",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000345",
       "meta" : {
         "definition" : {
-          "val" : "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.",
-          "xrefs" : [ "PMID:11377794" ]
+          "val" : "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Group_III_intron"
-        } ],
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "group III intron",
+          "val" : "expressed sequence tag",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "GO:0000374."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "group_III_intron"
+      "lbl" : "EST"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000369",
+      "id" : "http://purl.obolibrary.org/obo/so#maximally_overlaps",
       "meta" : {
+        "definition" : {
+          "val" : "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y.",
+          "xrefs" : [ "PMID:20226267" ]
+        },
+        "comments" : [ "Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-14T01:34:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "integrase_coding_region"
+      "type" : "PROPERTY",
+      "lbl" : "maximally_overlaps"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001216",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001675",
       "meta" : {
         "definition" : {
-          "val" : "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.",
+          "val" : "An A box within an RNA polymerase III type 1 promoter.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "endonuclease spliced intron",
+          "pred" : "hasRelatedSynonym",
+          "val" : "A box type 1",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-06T05:43:43Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "endonuclease_spliced_intron"
+      "lbl" : "A_box_type_1"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001215",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000344",
       "meta" : {
         "definition" : {
-          "val" : "The region of an exon that encodes for protein sequence.",
+          "val" : "Region of a transcript that regulates splicing.",
           "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "coding region of exon",
+          "val" : "splice enhancer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An exon containing either a start or stop codon will be partially coding and partially non coding."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_region_of_exon"
+      "lbl" : "splice_enhancer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001699",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000347",
       "meta" : {
         "definition" : {
-          "val" : "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/9628033" ]
+          "val" : "A match against a nucleotide sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "dCAPS primer",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "derived cleaved amplified polymorphic primer",
+          "val" : "nucleotide match",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-11-11T03:27:09Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dCAPS_primer"
+      "lbl" : "nucleotide_match"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000368",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001678",
       "meta" : {
         "definition" : {
-          "val" : "The junction in a genome where a transposable_element has inserted.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region.",
+          "xrefs" : [ "PMID:12381659" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "transposable element insertion site",
+          "pred" : "hasRelatedSynonym",
+          "val" : "regulatory promoter element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-07T04:39:48Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transposable_element_insertion_site"
+      "lbl" : "regulatory_promoter_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000286",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000346",
       "meta" : {
         "definition" : {
-          "val" : "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "Cre-Recombination target sequence.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Long_terminal_repeat"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "LTR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:long_terminal_repeat",
+          "pred" : "hasRelatedSynonym",
+          "val" : "Cre-recombination target region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "long terminal repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "direct terminal repeat",
+          "val" : "loxP site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -45311,143 +49798,141 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "long_terminal_repeat"
+      "lbl" : "loxP_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001133",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001677",
       "meta" : {
         "definition" : {
-          "val" : "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A core promoter region of RNA polymerase III type 1 promoters.",
+          "xrefs" : [ "PMID:12381659" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta turn",
+          "val" : "IE",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "intermediate element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00212"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-10-06T05:52:03Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn"
+      "lbl" : "intermediate_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001132",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000385",
       "meta" : {
         "definition" : {
-          "val" : "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "asx turn type right handed type one",
+          "val" : "INSDC_qualifier:RNase_MRP_RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "asx_turn_ir",
+          "val" : "RNase MRP RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00207"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "asx_turn_right_handed_type_one"
+      "lbl" : "RNase_MRP_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000285",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000115",
       "meta" : {
-        "definition" : {
-          "val" : "A gene that is foreign.",
-          "xrefs" : [ "SO:xp" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing complex 3D structural change",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "foreign gene",
+          "val" : "sequence variant causing complex 3D structural change",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001600"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "foreign_gene"
+      "lbl" : "sequence_variant_causing_complex_3D_structural_change"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000288",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001232",
       "meta" : {
         "definition" : {
-          "val" : "A fusion gene that is engineered.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A modified RNA base in which thymine is bound to the ribose ring.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "engineered fusion gene",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "The free molecule is CHEBI:30832." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_fusion_gene"
+      "lbl" : "ribothymidine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001135",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000384",
       "meta" : {
         "definition" : {
-          "val" : "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/OxyS_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta_turn_iil",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type II' turn",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type II' beta turn",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "beta turn left handed type two",
+          "val" : "OxyS RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00213"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_left_handed_type_two"
+      "lbl" : "OxyS_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000287",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001231",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is a fusion.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A modified RNA base in which guanine is methylated at the 7- position.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Fusion_gene"
-        } ],
+        "comments" : [ "The free molecule is CHEBI:2274." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "fusion gene",
+          "val" : "seven methylguanine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "7-methylguanine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -45456,53 +49941,64 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "fusion_gene"
+      "lbl" : "seven_methylguanine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001134",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000114",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_1000111"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_1000113",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_1000111"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000387",
       "meta" : {
         "definition" : {
-          "val" : "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/RprA_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "type I' turn",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "beta_turn_il",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "beta turn left handed type one",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type I' beta turn",
+          "val" : "RprA RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00215"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_left_handed_type_one"
+      "lbl" : "RprA_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000282",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001234",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA with a minus 1 frameshift.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute describing a feature that has either intra-genome or intracellular mobility.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mRNA with minus 1 frameshift",
-          "xrefs" : [ ]
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Mobile"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -45510,107 +50006,105 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_with_minus_1_frameshift"
+      "lbl" : "mobile"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000281",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000112",
       "meta" : {
-        "definition" : {
-          "val" : "A gene that is engineered and foreign.",
-          "xrefs" : [ "SO:xp" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered foreign gene",
+          "val" : "sequence variant causing no 3D structural change",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing no 3D structural change",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "engineered_foreign_gene"
+      "lbl" : "sequence_variant_causing_no_3D_structural_change"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001131",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000386",
       "meta" : {
         "definition" : {
-          "val" : "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Moved under enzymatic_RNA on 18 Nov 2021. See GitHub Issue #533." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "asx_turn_iir",
+          "val" : "RNase P RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "asx turn right handed type two",
+          "val" : "INSDC_qualifier:RNase_P_RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00205"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "asx_turn_right_handed_type_two"
+      "lbl" : "RNase_P_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000284",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001233",
       "meta" : {
         "definition" : {
-          "val" : "The recognition site is bipartite and interrupted.",
-          "xrefs" : [ "http://www.promega.com" ]
+          "val" : "A modified RNA base in which methylhypoxanthine is bound to the ribose ring.",
+          "xrefs" : [ "RSC:cb" ]
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "type_I_enzyme_restriction_site"
+      "lbl" : "methylinosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001130",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000119",
       "meta" : {
-        "definition" : {
-          "val" : "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "asx turn left handed type two",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing inactive ligand binding site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "asx_turn_iil",
+          "val" : "sequence variant causing inactive ligand binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00204"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001560"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "asx_turn_left_handed_type_two"
+      "lbl" : "sequence_variant_causing_inactive_ligand_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000283",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000381",
       "meta" : {
         "definition" : {
-          "val" : "A transposable_element that is engineered and foreign.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon.",
+          "xrefs" : [ "PMID:20463000" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered foreign transposable element gene",
+          "val" : "group IIA intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -45619,34 +50113,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_foreign_transposable_element_gene"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#variant_of",
-      "meta" : {
-        "definition" : {
-          "val" : "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.",
-          "xrefs" : [ "SO:immuno_workshop" ]
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added to SO during the immunology workshop, June 2007.  This relationship was approved by Barry Smith."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "variant_of"
+      "lbl" : "group_IIA_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000280",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000380",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is engineered.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs.",
+          "xrefs" : [ "PMID:2436805" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Hammerhead_ribozyme"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered gene",
+          "val" : "INSDC_qualifier:hammerhead_ribozyme",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "hammerhead ribozyme",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -45655,243 +50144,194 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_gene"
+      "lbl" : "hammerhead_ribozyme"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001129",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000118",
       "meta" : {
-        "definition" : {
-          "val" : "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "asx turn left handed type one",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing loss of function of polypeptide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "asx_turn_il",
+          "val" : "loss of function of polypeptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "sequence variant causing loss of function of polypeptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00206"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001559"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "asx_turn_left_handed_type_one"
+      "lbl" : "sequence_variant_causing_loss_of_function_of_polypeptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001126",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000117",
       "meta" : {
-        "definition" : {
-          "val" : "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "st motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "serine/threonine motif",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting polypeptide function",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "st_motif",
+          "val" : "sequence variant affecting polypeptide function",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00229"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001554"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "serine_threonine_motif"
+      "lbl" : "sequence_variant_affecting_polypeptide_function"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000279",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000383",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that is bound by a protein.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/MicF_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript bound by protein",
+          "val" : "MicF RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Formerly called transcript_by_bound_protein."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_bound_by_protein"
+      "lbl" : "MicF_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001125",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001230",
       "meta" : {
         "definition" : {
-          "val" : "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A modified RNA base in which hypoxanthine is bound to the ribose ring.",
+          "xrefs" : [ "RSC:cb", "http://library.med.utah.edu/RNAmods/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "The free molecule is CHEBI:17596." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Inosine"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "schellmann loop six",
+          "pred" : "hasRelatedSynonym",
+          "val" : "RNAMOD:017",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "six-residue schellmann loop",
+          "pred" : "hasRelatedSynonym",
+          "val" : "I",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00227"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "schellmann_loop_six"
+      "lbl" : "inosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000278",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000116",
       "meta" : {
-        "definition" : {
-          "val" : "A transcript that is bound by a nucleic acid.",
-          "xrefs" : [ "SO:xp" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript bound by nucleic acid",
+          "val" : "sequence variant causing conformational change",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing conformational change",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001601"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Formerly called transcript_by_bound_nucleic_acid."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "transcript_bound_by_nucleic_acid"
+      "lbl" : "sequence_variant_causing_conformational_change"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001128",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000382",
       "meta" : {
         "definition" : {
-          "val" : "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.",
-          "xrefs" : [ "EBIBS:GAR", "uniprot:feature_type" ]
+          "val" : "A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon.",
+          "xrefs" : [ "PMID:20463000" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "turn",
+          "pred" : "hasExactSynonym",
+          "val" : "group IIB intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00148"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_turn_motif"
+      "lbl" : "group_IIB_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001127",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001229",
       "meta" : {
         "definition" : {
-          "val" : "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "st_staple",
-          "xrefs" : [ ]
+        "comments" : [ "The free molecule is CHEBI:17802." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Pseudouridine"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "serine threonine staple motif",
-          "xrefs" : [ ]
+          "val" : "RNAMOD:050"
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00230"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "serine_threonine_staple_motif"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001122",
-      "meta" : {
-        "definition" : {
-          "val" : "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide nest right left motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nest_right_left",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nest_rl",
-          "xrefs" : [ ]
+          "val" : " Y",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00225"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_nest_right_left_motif"
+      "lbl" : "pseudouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000275",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001228",
       "meta" : {
         "definition" : {
-          "val" : "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.",
-          "xrefs" : [ "GOC:kgc" ]
+          "val" : "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/SnoRNA"
+          "val" : "http://en.wikipedia.org/wiki/Dihydrouridine"
+        }, {
+          "val" : "RNAMOD:051"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "small nucleolar RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:snoRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
+          "val" : " D",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#RNAMOD"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -45899,245 +50339,184 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "snoRNA"
+      "lbl" : "dihydrouridine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000274",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000122",
       "meta" : {
-        "definition" : {
-          "val" : "A small nuclear RNA molecule involved in pre-mRNA splicing and processing.",
-          "xrefs" : [ "PMID:11733745", "WB:ems", "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/SnRNA"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "small nuclear RNA",
+          "val" : "sequence variant causing polypeptide post translational processing change",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing polypeptide post translational processing change",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:snRNA",
+          "val" : "polypeptide post-translational processing affected",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001562"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "snRNA"
+      "lbl" : "sequence_variant_causing_polypeptide_post_translational_processing_change"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001121",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000378",
       "meta" : {
         "definition" : {
-          "val" : "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/DsrA_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide nest left right motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nest_left_right",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nest_lr",
+          "val" : "DsrA RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00224"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_nest_left_right_motif"
+      "lbl" : "DsrA_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000277",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001225",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence that is bound by another molecule.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that is silenced by histone modification.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bound by factor",
+          "val" : "gene silenced by histone modification",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Formerly called transcript_by_bound_factor."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bound_by_factor"
+      "lbl" : "gene_silenced_by_histone_modification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001124",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000121",
       "meta" : {
-        "definition" : {
-          "val" : "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "schellmann loop seven",
+          "val" : "sequence variant causing polypeptide localization change",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "seven-residue schellmann loop",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing polypeptide localization change",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001558"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00228"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "schellmann_loop_seven"
+      "lbl" : "sequence_variant_causing_polypeptide_localization_change"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001123",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000377",
       "meta" : {
         "definition" : {
-          "val" : "A motif of six or seven consecutive residues that contains two H-bonds.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "paperclip loop",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "paperclip",
+          "pred" : "hasExactSynonym",
+          "val" : "CsrB RsmB RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "schellmann loop",
+          "val" : "CsrB-RsmB RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00226"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "schellmann_loop"
+      "lbl" : "CsrB_RsmB_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000276",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001224",
       "meta" : {
         "definition" : {
-          "val" : "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.",
-          "xrefs" : [ "PMID:11081512", "PMID:12592000" ]
+          "val" : "A gene that is silenced by RNA interference.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/StRNA"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/MiRNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "small temporal RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "micro RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:miRNA",
+          "val" : "RNAi silenced gene",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "stRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
+          "val" : "gene silenced by RNA interference",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "microRNA",
+          "val" : "RNA interference silenced gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0000649"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miRNA"
+      "lbl" : "gene_silenced_by_RNA_interference"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000271",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000120",
       "meta" : {
-        "definition" : {
-          "val" : "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.",
-          "xrefs" : [ "SO:ke" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tryptophanyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "tryptophanyl-transfer ribonucleic acid",
+          "val" : "sequence variant causing inactive catalytic site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "tryptophanyl tRNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing inactive catalytic site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001618"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "tryptophanyl_tRNA"
+      "lbl" : "sequence_variant_causing_inactive_catalytic_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000270",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001227",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that is silenced by histone deacetylation.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "threonyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "threonyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "threonyl-transfer ribonucleic acid",
+          "val" : "gene silenced by histone deacetylation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -46146,56 +50525,39 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "threonyl_tRNA"
+      "lbl" : "gene_silenced_by_histone_deacetylation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001120",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001226",
       "meta" : {
         "definition" : {
-          "val" : "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A gene that is silenced by histone methylation.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nest_motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "nest",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "polypeptide nest motif",
+          "val" : "gene silenced by histone methylation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00223"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_nest_motif"
+      "lbl" : "gene_silenced_by_histone_methylation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000273",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000379",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a valine anticodon, and a 3' valine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/GcvB_RNA"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "valyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "valyl tRNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "valyl-transfer ribonucleic acid",
+          "val" : "GcvB RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -46204,122 +50566,85 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "valyl_tRNA"
+      "lbl" : "GcvB_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000272",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000104",
       "meta" : {
-        "definition" : {
-          "val" : "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.",
-          "xrefs" : [ "SO:ke" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tyrosyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "tyrosyl tRNA",
+          "val" : "sequence variant increasing level of translation product",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "tyrosyl-transfer RNA",
+          "val" : "mutationt increasing level of translation product",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "tyrosyl_tRNA"
+      "lbl" : "sequence_variant_increasing_level_of_translation_product"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001119",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000374",
       "meta" : {
         "definition" : {
-          "val" : "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An RNA with catalytic activity.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/310_helix"
+          "val" : "http://en.wikipedia.org/wiki/Ribozyme"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "three ten helix",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "310 helix",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "3-10 helix",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "3(10) helix",
+          "val" : "INSDC_qualifier:ribozyme",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:0000340"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_ten_helix"
+      "lbl" : "ribozyme"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001118",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001221",
       "meta" : {
         "definition" : {
-          "val" : "The pi helix has 4.1 residues per turn and a translation of 1.15  (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An attribute describing an epigenetic process where a gene is inactivated by histone modification.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Pi_helix"
-        } ],
+        "comments" : [ "Histone modification is GO:0016570." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pi helix",
+          "val" : "silenced by histone modification",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00153"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pi_helix"
+      "lbl" : "silenced_by_histone_modification"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000268",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000373",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a proline anticodon, and a 3' proline binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A recombinationally rearranged gene by inversion.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "prolyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "prolyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "prolyl-transfer ribonucleic acid",
+          "val" : "recombinationally inverted gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -46328,241 +50653,216 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "prolyl_tRNA"
+      "lbl" : "recombinationally_inverted_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001115",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000103",
       "meta" : {
-        "definition" : {
-          "val" : "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.",
-          "xrefs" : [ "EBIBS:GAR" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "helix-l",
+          "val" : "mutationdecreasing level of translation product",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "left handed helix",
+          "val" : "sequence variant decreasing level of translation product",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00222"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001555"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "left_handed_peptide_helix"
+      "lbl" : "sequence_variant_decreasing_level_of_translation_product"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001599",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001220",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the resulting polypeptide structure.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An attribute describing an epigenetic process where a gene is inactivated by RNA interference.",
+          "xrefs" : [ "RSC:cb" ]
         },
+        "comments" : [ "RNA interference is GO:0016246." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3D polypeptide structure variant",
+          "val" : "silenced by RNA interference",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:44:46Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "3D_polypeptide_structure_variant"
+      "lbl" : "silenced_by_RNA_interference"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001114",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000376",
       "meta" : {
         "definition" : {
-          "val" : "A helix is a secondary_structure conformation where the peptide backbone forms a coil.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/6S_RNA"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "helix",
+          "pred" : "hasExactSynonym",
+          "val" : "6S RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RNA 6S",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00152"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "peptide_helix"
+      "lbl" : "RNA_6S"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001598",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001223",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant within the transcript that changes the structure of the translational product.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
+        "comments" : [ "Histone deacetylation is GO:0016573." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translational product structure variant",
+          "val" : "silenced by histone deacetylation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:44:17Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translational_product_structure_variant"
+      "lbl" : "silenced_by_histone_deacetylation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000267",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000102",
       "meta" : {
-        "definition" : {
-          "val" : "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.",
-          "xrefs" : [ "SO:ke" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "phenylalanyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "phenylalanyl-transfer ribonucleic acid",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting level of translational product",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "phenylalanyl tRNA",
+          "val" : "sequence variant affecting level of translational product",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001553"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "phenylalanyl_tRNA"
+      "lbl" : "sequence_variant_affecting_level_of_translational_product"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001117",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000101",
       "meta" : {
         "definition" : {
-          "val" : "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : ".",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Alpha_helix"
-        } ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "helix",
-          "xrefs" : [ "uniprot:feature_type" ]
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide C-terminal elongation",
+          "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "a-helix",
+          "pred" : "hasExactSynonym",
+          "val" : "mutation causing polypeptide C terminal elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001610"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00040"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "alpha_helix"
+      "lbl" : "mutation_causing_polypeptide_C_terminal_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#processed_into",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000375",
       "meta" : {
         "definition" : {
-          "val" : "X is processed_into Y if a region X is modified to create Y.",
-          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
+          "val" : "Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.",
+          "xrefs" : [ "https://rfam.xfam.org/family/RF00002" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: miRNA_primary_transcript processed into miRNA."
+        "comments" : [ "Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic rRNA 5 8S",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T12:15:02Z"
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 5.8S LSU rRNA",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 5.8S ribosomal RNA",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 5.8S rRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "processed_into"
+      "type" : "CLASS",
+      "lbl" : "cytosolic_5_8S_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001116",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001222",
       "meta" : {
         "definition" : {
-          "val" : "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An attribute describing an epigenetic process where a gene is inactivated by histone methylation.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Histone methylation is GO:0016571." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "right handed helix",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "helix",
+          "val" : "silenced by histone methylation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:0000339"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "right_handed_peptide_helix"
+      "lbl" : "silenced_by_histone_methylation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000269",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000370",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a serine anticodon, and a 3' serine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others).",
+          "xrefs" : [ "PMID:28541282", "PomBase:al", "SO:ma" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "seryl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "seryl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "seryl-transfer ribonucleic acid",
+          "val" : "small regulatory ncRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -46571,264 +50871,196 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "seryl_tRNA"
+      "lbl" : "small_regulatory_ncRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001155",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000108",
       "meta" : {
-        "definition" : {
-          "val" : "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.",
-          "xrefs" : [ "PMID:2371257", "SO:cb" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta turn type eight",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type VIII turn",
+          "val" : "mutaton causing inframe polypeptide C terminal elongation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "type VIII beta turn",
+          "val" : "inframe_polypeptide C-terminal elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001612"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_type_eight"
+      "lbl" : "mutaton_causing_inframe_polypeptide_C_terminal_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002003",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000107",
       "meta" : {
-        "definition" : {
-          "val" : "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR).",
-          "xrefs" : [ "SGD:jd" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Z2-segment",
+          "val" : "out of frame polypeptide N-terminal elongation",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mutation causing out of frame polypeptide N terminal elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:36:45Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Janos Demeter, SGD."
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001615"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "Z2_region"
+      "lbl" : "mutation_causing_out_of_frame_polypeptide_N_terminal_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002004",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000372",
       "meta" : {
         "definition" : {
-          "val" : "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS.",
-          "xrefs" : [ "SGD:jd" ]
+          "val" : "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein.",
+          "xrefs" : [ "RSC:cb" ]
         },
+        "comments" : [ "This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. Moved under ncRNA on 18 Nov 2021. See GitHub Issue #533." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ACS",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ARS consensus sequence",
+          "val" : "enzymatic RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:47:48Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ARS_consensus_sequence"
+      "lbl" : "enzymatic_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001154",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000106",
       "meta" : {
-        "definition" : {
-          "val" : "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.",
-          "xrefs" : [ "PMID:2371257", "SO:cb" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta turn type six b",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type VIb turn",
+          "val" : "inframe polypeptide N-terminal elongation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "type VIb beta turn",
+          "val" : "mutation causing inframe polypeptide N terminal elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001614"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_type_six_b"
+      "lbl" : "mutation_causing_inframe_polypeptide_N_terminal_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001157",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000105",
       "meta" : {
-        "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).",
-          "xrefs" : [ "PMID:16827941:12537576" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "DMv4",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "motif 1 element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "promoter motif 1",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "YGGTCACATR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "directional motif v4",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting polypeptide amino acid sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DMv4 motif",
+          "val" : "sequence variant affecting polypeptide amino acid sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001603"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "DMv4_motif"
+      "lbl" : "sequence_variant_affecting_polypeptide_amino_acid_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002001",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000371",
       "meta" : {
         "definition" : {
-          "val" : "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha).",
-          "xrefs" : [ "SGD:jd" ]
+          "val" : "A transposon that encodes function required for conjugation.",
+          "xrefs" : [ "http://www.sci.sdsu.edu/~smaloy/Glossary/C.html" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Y-region",
+          "val" : "conjugative transposon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:33:30Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Janos Demeter, SGD."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Y_region"
+      "lbl" : "conjugative_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001156",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000109",
       "meta" : {
-        "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.",
-          "xrefs" : [ "PMID:12537576" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DRE motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "WATCGATW_motif",
+          "val" : "out of frame polypeptide C-terminal elongation",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "NDM4",
+          "val" : "mutation causing out of frame polypeptide C terminal elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183.  Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10."
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001613"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "DRE_motif"
+      "lbl" : "mutation_causing_out_of_frame_polypeptide_C_terminal_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002002",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001218",
       "meta" : {
         "definition" : {
-          "val" : "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR).",
-          "xrefs" : [ "SGD:jd" ]
+          "val" : "An insertion that derives from another organism, via the use of recombinant DNA technology.",
+          "xrefs" : [ "SO:bm" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Z1-region",
+          "val" : "transgenic insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:34:59Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Janos Demeter, SGD."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Z1_region"
+      "lbl" : "transgenic_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001151",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001217",
       "meta" : {
         "definition" : {
-          "val" : "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.",
-          "xrefs" : [ "PMID:2371257", "SO:cb" ]
+          "val" : "A gene that codes for an RNA that can be translated into a protein.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#Alliance_of_Genome_Resources" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "type VIa turn",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "beta turn type six a",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type VIa beta turn",
+          "val" : "protein coding gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -46837,244 +51069,186 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_type_six_a"
+      "lbl" : "protein_coding_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001150",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001219",
       "meta" : {
         "definition" : {
-          "val" : "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.",
-          "xrefs" : [ "SO:cb" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "beta turn type six",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type VI turn",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type VI beta turn",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "cis-proline loop",
+          "val" : "A gene that has been produced as the product of a reverse transcriptase mediated event.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_type_six"
+      "lbl" : "retrogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001153",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000111",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "definition" : {
+          "val" : "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "type VIa2 beta turn",
+          "val" : "sequence variant affecting 3D-structure of polypeptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing uncharacterised 3D structural change",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "beta turn type six a two",
+          "val" : "sequence variant causing partially characterised 3D structural change",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "type VIa2 turn",
+          "val" : "sequence variant causing uncharacterised 3D structural change",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "beta_turn_type_six_a_two"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001152",
-      "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation causing partially characterised 3D structural change",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "type VIa1 beta turn",
+          "val" : "sequence variant affecting 3D structure of polypeptide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "beta turn type six a one",
+          "val" : "sequence_variant_causing_partially_characterised_3D_structural_change",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "mutation affecting 3D structure of polypeptide",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "type VIa1 turn",
+          "val" : "sequence_variant_causing_uncharacterised_3D_structural_change",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001599"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000113"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000114"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_type_six_a_one"
+      "lbl" : "sequence_variant_affecting_3D_structure_of_polypeptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#lost",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001214",
       "meta" : {
         "definition" : {
-          "val" : "X lost Y if X is a variant_of X' and Y part of X' but not X.",
+          "val" : "The maximal intersection of exon and UTR.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "noncoding region of exon",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2011-06-28T12:53:16Z"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "lost"
+      "type" : "CLASS",
+      "lbl" : "noncoding_region_of_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001148",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001698",
       "meta" : {
         "definition" : {
-          "val" : "Site which has been experimentally altered.",
-          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+          "val" : "\"A primer containing an SNV at the 3' end for accurate genotyping.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/11252801" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mutagen",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mutagenesis",
+          "val" : "ASPE primer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "mutated_site",
+          "val" : "allele specific primer extension primer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00036"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-11-11T03:25:21Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mutated_variant_site"
+      "lbl" : "ASPE_primer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001147",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000367",
       "meta" : {
         "definition" : {
-          "val" : "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.",
-          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+          "val" : "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.",
+          "xrefs" : [ "SO:as" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "natural_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "variant",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "sequence variation",
+          "pred" : "hasExactSynonym",
+          "val" : "attI site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00071"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "natural_variant_site"
+      "lbl" : "attI_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001149",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000366",
       "meta" : {
         "definition" : {
-          "val" : "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.",
-          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+          "val" : "The junction where an insertion occurred.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "alternative_sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "isoform",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "varsplic",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "sequence variation",
+          "val" : "insertion site",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "var_seq",
-          "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00073"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001065"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alternate_sequence_site"
+      "lbl" : "insertion_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000297",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001213",
       "meta" : {
         "definition" : {
-          "val" : "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile.",
+          "xrefs" : [ "PMID:11377794" ]
         },
+        "comments" : [ "GO:0000374." ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/D_loop"
+          "val" : "http://en.wikipedia.org/wiki/Group_III_intron"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:D-loop",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "D-loop",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "displacement loop",
+          "val" : "group III intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47083,83 +51257,66 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "D_loop"
+      "lbl" : "group_III_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001144",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001697",
       "meta" : {
         "definition" : {
-          "val" : "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A region of sequence identified by CHiP seq technology to contain a protein binding site.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "st_turn_ir",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "st turn right handed type one",
+          "pred" : "hasRelatedSynonym",
+          "val" : "ChIP seq region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00235"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-11-02T11:43:07Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "st_turn_right_handed_type_one"
+      "lbl" : "ChIP_seq_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001143",
+      "id" : "http://purl.obolibrary.org/obo/SO_1000110",
       "meta" : {
         "definition" : {
-          "val" : "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "st turn left handed type two",
+          "val" : "frame restoring sequence variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "st_turn_iil",
+          "val" : "frame restoring mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00232"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "st_turn_left_handed_type_two"
+      "lbl" : "frame_restoring_sequence_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000296",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001216",
       "meta" : {
         "definition" : {
-          "val" : "A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites.",
-          "xrefs" : [ "NCBI:cf", "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Origin_of_replication"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "origin of replication",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ori",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:rep_origin",
+          "val" : "endonuclease spliced intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47168,39 +51325,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "origin_of_replication"
+      "lbl" : "endonuclease_spliced_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001146",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000369",
       "meta" : {
-        "definition" : {
-          "val" : "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.",
-          "xrefs" : [ "EBIBS:GAR", "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "sequence_variations",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00336"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_variation_site"
+      "lbl" : "integrase_coding_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000299",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000368",
       "meta" : {
+        "definition" : {
+          "val" : "The junction in a genome where a transposable_element has inserted.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "specific recombination site",
+          "val" : "transposable element insertion site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47209,48 +51356,48 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "specific_recombination_site"
+      "lbl" : "transposable_element_insertion_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001145",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001699",
       "meta" : {
         "definition" : {
-          "val" : "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/pubmed/9628033" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "st_turn_iir",
+          "val" : "derived cleaved amplified polymorphic primer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "st turn right handed type two",
+          "val" : "dCAPS primer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00233"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-11-11T03:27:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "st_turn_right_handed_type_two"
+      "lbl" : "dCAPS_primer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000298",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001215",
       "meta" : {
+        "definition" : {
+          "val" : "The region of an exon that encodes for protein sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "An exon containing either a start or stop codon will be partially coding and partially non coding." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_recomb",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "recombination feature",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:other",
+          "val" : "coding region of exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47259,18 +51406,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombination_feature"
+      "lbl" : "coding_region_of_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001140",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001133",
       "meta" : {
         "definition" : {
-          "val" : "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.",
+          "val" : "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization.",
           "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gamma turn inverse",
+          "val" : "beta turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47278,122 +51425,59 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00221"
+          "val" : "BS:00212"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gamma_turn_inverse"
+      "lbl" : "beta_turn"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000293",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000286",
       "meta" : {
         "definition" : {
-          "val" : "A repetitive element that is engineered and foreign.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Long_terminal_repeat"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "engineered foreign repetitive element",
+          "pred" : "hasRelatedSynonym",
+          "val" : "direct terminal repeat",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "engineered_foreign_repetitive_element"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000292",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "repetitive_element"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000295",
-      "meta" : {
-        "definition" : {
-          "val" : "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.",
-          "xrefs" : [ "PMID:9428511" ]
-        },
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "U12-dependent intron",
+          "val" : "long terminal repeat",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U12 intron",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "May have either GT-AC or AT-AC 5' and 3' boundaries."
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "U12_intron"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001142",
-      "meta" : {
-        "definition" : {
-          "val" : "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "st turn left handed type one",
+          "val" : "LTR",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "st_turn_il",
+          "val" : "INSDC_qualifier:long_terminal_repeat",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00234"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "st_turn_left_handed_type_one"
+      "lbl" : "long_terminal_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000294",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000285",
       "meta" : {
         "definition" : {
-          "val" : "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that is foreign.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Inverted_repeat"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inverted repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:inverted",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "inverted repeat sequence",
+          "val" : "foreign gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47402,52 +51486,44 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inverted_repeat"
+      "lbl" : "foreign_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001141",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001132",
       "meta" : {
         "definition" : {
-          "val" : "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).",
+          "val" : "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
           "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "st_turn",
+          "val" : "asx_turn_ir",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "serine/threonine turn",
+          "val" : "asx turn type right handed type one",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00231"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00207"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "serine_threonine_turn"
+      "lbl" : "asx_turn_right_handed_type_one"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000291",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000288",
       "meta" : {
+        "definition" : {
+          "val" : "A fusion gene that is engineered.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "dinucleotide repeat microsatellite marker",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "trinucleotide repeat microsatellite locus",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "trinucleotide repeat microsatellite feature",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "rinucleotide repeat microsatellite",
+          "val" : "engineered fusion gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47456,57 +51532,65 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "trinucleotide_repeat_microsatellite_feature"
+      "lbl" : "engineered_fusion_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000290",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001135",
       "meta" : {
+        "definition" : {
+          "val" : "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "dinucleotide repeat microsatellite marker",
+          "val" : "beta_turn_iil",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "dinucleotide repeat microsatellite locus",
+          "val" : "beta turn left handed type two",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "dinucleotide repeat microsatellite feature",
+          "val" : "type II' beta turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "dinucleotide repeat microsatellite",
+          "val" : "type II' turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00213"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dinucleotide_repeat_microsatellite_feature"
+      "lbl" : "beta_turn_left_handed_type_two"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001137",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001134",
       "meta" : {
         "definition" : {
-          "val" : "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
+          "val" : "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees.",
           "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta_turn_iir",
+          "val" : "type I' turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "type II beta turn",
+          "val" : "beta_turn_il",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "beta turn right handed type two",
+          "val" : "beta turn left handed type one",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "type II turn",
+          "val" : "type I' beta turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47514,45 +51598,24 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00214"
+          "val" : "BS:00215"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_right_handed_type_two"
+      "lbl" : "beta_turn_left_handed_type_one"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000289",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000287",
       "meta" : {
         "definition" : {
-          "val" : "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.",
-          "xrefs" : [ "NCBI:th", "http://www.informatics.jax.org/silver/glossary.shtml" ]
+          "val" : "A gene that is a fusion.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Microsatellite"
+          "val" : "http://en.wikipedia.org/wiki/Fusion_gene"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:microsatellite",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "microsatellite locus",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "STR",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/" ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "short tandem repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "microsatellite marker",
+          "val" : "fusion gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47561,80 +51624,60 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "microsatellite"
+      "lbl" : "fusion_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001136",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000282",
       "meta" : {
         "definition" : {
-          "val" : "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "An mRNA with a minus 1 frameshift.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta_turn_ir",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "beta turn right handed type one",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type I turn",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "type I beta turn",
+          "val" : "mRNA with minus 1 frameshift",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00216"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_turn_right_handed_type_one"
+      "lbl" : "mRNA_with_minus_1_frameshift"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001139",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000281",
       "meta" : {
         "definition" : {
-          "val" : "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A gene that is engineered and foreign.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gamma turn classic",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "classic gamma turn",
+          "val" : "engineered foreign gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00220"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gamma_turn_classic"
+      "lbl" : "engineered_foreign_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001138",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001131",
       "meta" : {
         "definition" : {
-          "val" : "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.",
+          "val" : "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
           "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gamma turn",
+          "val" : "asx_turn_iir",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "asx turn right handed type two",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47642,99 +51685,97 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00219"
+          "val" : "BS:00205"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gamma_turn"
+      "lbl" : "asx_turn_right_handed_type_two"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002025",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000284",
       "meta" : {
         "definition" : {
-          "val" : "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I.",
-          "xrefs" : [ "PMID:22582262", "PMID:23117617", "PMID:24173580", "PomBase:vw" ]
+          "val" : "The recognition site is bipartite and interrupted.",
+          "xrefs" : [ "http://www.promega.com" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "type_I_enzyme_restriction_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000283",
+      "meta" : {
+        "definition" : {
+          "val" : "A transposable_element that is engineered and foreign.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cis-acting homologous chromosome pairing region",
+          "val" : "engineered foreign transposable element gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-07-14T11:40:34Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the \"Mei2 dot\". This term was Requested by Val Wood, PomBase."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cis_acting_homologous_chromosome_pairing_region"
+      "lbl" : "engineered_foreign_transposable_element_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001177",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001130",
       "meta" : {
         "definition" : {
-          "val" : "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.",
-          "xrefs" : [ "ISBN:0716719207" ]
+          "val" : "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TpsiC loop",
+          "val" : "asx turn left handed type two",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "T loop",
+          "val" : "asx_turn_iil",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00204"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "T_loop"
+      "lbl" : "asx_turn_left_handed_type_two"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002026",
+      "id" : "http://purl.obolibrary.org/obo/so#variant_of",
       "meta" : {
         "definition" : {
-          "val" : "The nucleotide sequence which encodes the intein portion of the precursor gene.",
-          "xrefs" : [ "PMID:8165123" ]
+          "val" : "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A.",
+          "xrefs" : [ "SO:immuno_workshop" ]
         },
+        "comments" : [ "Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-07-14T11:53:21Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Janos Demeter 2014."
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "intein_encoding_region"
+      "type" : "PROPERTY",
+      "lbl" : "variant_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001176",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000280",
       "meta" : {
         "definition" : {
-          "val" : "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.",
-          "xrefs" : [ "ISBN:071671920" ]
+          "val" : "A gene that is engineered.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "D loop",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "DHU loop",
+          "val" : "engineered gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47743,110 +51784,76 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DHU_loop"
+      "lbl" : "engineered_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001179",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001129",
       "meta" : {
         "definition" : {
-          "val" : "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012" ]
+          "val" : "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "U3 small nucleolar RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small nucleolar RNA U3",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "U3 snoRNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "asx_turn_il",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snoRNA U3",
+          "val" : "asx turn left handed type one",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The definition is most of the old definition for snoRNA (SO:0000275)."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00206"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "U3_snoRNA"
+      "lbl" : "asx_turn_left_handed_type_one"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002023",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001126",
       "meta" : {
         "definition" : {
-          "val" : "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library.",
-          "xrefs" : [ "OBO:prs", "PMID:22574170" ]
+          "val" : "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "multiplexing sequence identifier",
+          "val" : "serine/threonine motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "st motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "st_motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00229"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-05-30T15:13:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "multiplexing_sequence_identifier"
+      "lbl" : "serine_threonine_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002024",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000279",
       "meta" : {
         "definition" : {
-          "val" : "The leftmost segment of homology in the HML and MAT mating loci,  but not present in HMR.",
-          "xrefs" : [ "SGD:jd" ]
+          "val" : "A transcript that is bound by a protein.",
+          "xrefs" : [ "SO:xp" ]
         },
+        "comments" : [ "Formerly called transcript_by_bound_protein." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "W-region",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "MERGED COMMENT:\nTARGET COMMENT: Requested by Janos Demeter, SGD.\n--------------------\nSOURCE COMMENT: Requested by Janos Demeter, SGD."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0002000"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-07-11T13:20:08Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "W_region"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001178",
-      "meta" : {
-        "definition" : {
-          "val" : "A primary transcript encoding pyrrolysyl tRNA (SO:0000766).",
-          "xrefs" : [ "RSC:cb" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "pyrrolysine tRNA primary transcript",
+          "val" : "transcript bound by protein",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47855,116 +51862,126 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pyrrolysine_tRNA_primary_transcript"
+      "lbl" : "transcript_bound_by_protein"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002021",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000278",
       "meta" : {
         "definition" : {
-          "val" : "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.",
-          "xrefs" : [ "PMID:17614787" ]
+          "val" : "A transcript that is bound by a nucleic acid.",
+          "xrefs" : [ "SO:xp" ]
         },
+        "comments" : [ "Formerly called transcript_by_bound_nucleic_acid." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mating type region replication fork barrier",
+          "val" : "transcript bound by nucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-05-30T14:57:26Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Midori Harris."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mating_type_region_replication_fork_barrier"
+      "lbl" : "transcript_bound_by_nucleic_acid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001173",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001125",
       "meta" : {
         "definition" : {
-          "val" : "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.",
-          "xrefs" : [ "ISBN:0716719207" ]
+          "val" : "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4).",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "anticodon loop",
+          "val" : "schellmann loop six",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "anti-codon loop",
+          "val" : "six-residue schellmann loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00227"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "anticodon_loop"
+      "lbl" : "schellmann_loop_six"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002022",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001128",
       "meta" : {
         "definition" : {
-          "val" : "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts.",
-          "xrefs" : [ "PMID:20178743", "PMID:24095277", "PomBase:al" ]
+          "val" : "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues.",
+          "xrefs" : [ "EBIBS:GAR", "uniprot:feature_type" ]
         },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "primal small RNA",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "turn",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-05-30T15:01:24Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00148"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "priRNA"
+      "lbl" : "polypeptide_turn_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001172",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001127",
       "meta" : {
         "definition" : {
-          "val" : "A region of a tRNA.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tRNA region",
+          "val" : "serine threonine staple motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "st_staple",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00230"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tRNA_region"
+      "lbl" : "serine_threonine_staple_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001175",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000275",
       "meta" : {
         "definition" : {
-          "val" : "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.",
-          "xrefs" : [ "ISBN:0716719207" ]
+          "val" : "Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing.",
+          "xrefs" : [ "GOC:kgc", "PMID:31828325" ]
         },
+        "comments" : [ "Updated the definition of snoRNA (SO:0000275) from \"A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.\" to \"Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing.\" to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "CCA tail",
+          "val" : "small nucleolar RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "CCA sequence",
+          "val" : "INSDC_qualifier:snoRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -47973,164 +51990,112 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CCA_tail"
+      "lbl" : "snoRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002020",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001122",
       "meta" : {
         "definition" : {
-          "val" : "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions.",
-          "xrefs" : [ "PMID:24013502" ]
+          "val" : "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "boundary element",
+          "val" : "nest_rl",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "insulator",
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide nest right left motif",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Antonia Lock. Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf)."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-05-30T14:45:37Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "boundary_element"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001174",
-      "meta" : {
-        "definition" : {
-          "val" : "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.",
-          "xrefs" : [ "RSC:cb" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Anticodon"
-        } ],
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "anti-codon",
+          "val" : "nest_right_left",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00225"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "anticodon"
+      "lbl" : "polypeptide_nest_right_left_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001171",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001121",
       "meta" : {
         "definition" : {
-          "val" : "A component of the large ribosomal subunit in mitochondrial rRNA.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA 21S",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "21S LSU rRNA",
+          "val" : "polypeptide nest left right motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "21S ribosomal RNA",
+          "val" : "nest_left_right",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "21S rRNA",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "rRNA_21S"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001170",
-      "meta" : {
-        "definition" : {
-          "val" : "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.",
-          "xrefs" : [ "PMID:16537396" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "maverick element",
+          "val" : "nest_lr",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00224"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polinton"
+      "lbl" : "polypeptide_nest_left_right_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002018",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000274",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant occurring within a conserved region of an intron.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A small nuclear RNA molecule involved in pre-mRNA splicing and processing.",
+          "xrefs" : [ "PMID:11733745", "WB:ems", "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+          "val" : "http://en.wikipedia.org/wiki/SnRNA"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:conserved_intron_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conserved intron variant",
+          "val" : "small nuclear RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:INTRON_CONSERVED",
+          "val" : "INSDC_qualifier:snRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Uma Paila (UVA) for snpEff."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-25T02:58:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conserved_intron_variant"
+      "lbl" : "snRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001169",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000277",
       "meta" : {
         "definition" : {
-          "val" : "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.",
+          "val" : "An attribute describing a sequence that is bound by another molecule.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Formerly called transcript_by_bound_factor." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "double stranded RNA virus sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ds RNA viral sequence",
+          "val" : "bound by factor",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48139,142 +52104,159 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ds_RNA_viral_sequence"
+      "lbl" : "bound_by_factor"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002019",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001124",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where at least one base in the start codon is changed, but the start remains.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5).",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:SYNONYMOUS_START",
+          "val" : "schellmann loop seven",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "seven-residue schellmann loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-28T10:08:41Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00228"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "start_retained_variant"
+      "lbl" : "schellmann_loop_seven"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002016",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001123",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of six or seven consecutive residues that contains two H-bonds.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "paperclip",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "3 prime UTR elongation",
+          "val" : "schellmann loop",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "paperclip loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-25T10:55:33Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00226"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "3_prime_UTR_elongation"
+      "lbl" : "schellmann_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002017",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000276",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located in a conserved intergenic region, between genes.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.",
+          "xrefs" : [ "PMID:11081512", "PMID:12592000" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+          "val" : "http://en.wikipedia.org/wiki/StRNA"
+        }, {
+          "val" : "http://en.wikipedia.org/wiki/MiRNA"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:conserved_intergenic_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "stRNA",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conserved intergenic variant",
+          "val" : "micro RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:INTERGENIC_CONSERVED",
+          "val" : "microRNA",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Uma Paila (UVA) for snpEff."
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:miRNA",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-25T02:54:39Z"
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small temporal RNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0000649"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conserved_intergenic_variant"
+      "lbl" : "miRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002014",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000271",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence.",
+          "val" : "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5 prime UTR elongation",
+          "val" : "tryptophanyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "tryptophanyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "tryptophanyl tRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-25T10:48:26Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_elongation"
+      "lbl" : "tryptophanyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001166",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000270",
       "meta" : {
         "definition" : {
-          "val" : "A non directional promoter motif with consensus sequence GAGAGCG.",
-          "xrefs" : [ "PMID:16827941" ]
+          "val" : "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "GAGA motif",
+          "val" : "threonyl tRNA",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "NDM1",
+          "pred" : "hasRelatedSynonym",
+          "val" : "threonyl-transfer RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "GAGA",
+          "val" : "threonyl-transfer ribonucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48283,192 +52265,177 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "GAGA_motif"
+      "lbl" : "threonyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001165",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001120",
       "meta" : {
         "definition" : {
-          "val" : "A promoter motif with consensus sequence CARCCCT.",
-          "xrefs" : [ "PMID:16827941" ]
+          "val" : "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DMv1 motif",
+          "val" : "nest_motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "directional promoter motif v1",
+          "val" : "polypeptide nest motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "DMv1",
-          "xrefs" : [ ]
+          "val" : "nest",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00223"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DMv1_motif"
+      "lbl" : "polypeptide_nest_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002015",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000273",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes the reduction of a the 3' UTR  with regard to the reference sequence.",
+          "val" : "A tRNA sequence that has a valine anticodon, and a 3' valine binding region.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:3_prime_utr_truncation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "valyl-transfer RNA",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:UTR_3_DELETED",
+          "val" : "valyl tRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "3 prime UTR truncation",
+          "val" : "valyl-transfer ribonucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-25T10:54:50Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "3_prime_UTR_truncation"
+      "lbl" : "valyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002012",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000272",
       "meta" : {
         "definition" : {
-          "val" : "A codon variant that changes at least one base of the canonical start codon.",
+          "val" : "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:start_lost",
+          "pred" : "hasRelatedSynonym",
+          "val" : "tyrosyl-transfer RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:start_lost",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "tyrosyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:START_LOST",
+          "val" : "tyrosyl tRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Request from  Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-24T02:41:28Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "start_lost"
+      "lbl" : "tyrosyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001168",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001119",
       "meta" : {
         "definition" : {
-          "val" : "A non directional promoter motif with consensus sequence GAAAGCT.",
-          "xrefs" : [ "PMID:16827941" ]
+          "val" : "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/310_helix"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non directional motif 3",
+          "val" : "three ten helix",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "NDM3 motif",
+          "val" : "310 helix",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "NDM3",
+          "val" : "3-10 helix",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3(10) helix",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:0000340"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "NDM3_motif"
+      "lbl" : "three_ten_helix"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002013",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001118",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes the reduction of a the 5'UTR  with regard to the reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+          "val" : "http://en.wikipedia.org/wiki/Pi_helix"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:5_prime_utr_truncation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5 prime UTR truncation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:UTR_5_DELETED",
+          "val" : "pi helix",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-25T10:46:42Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00153"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_truncation"
+      "lbl" : "pi_helix"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001167",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000268",
       "meta" : {
         "definition" : {
-          "val" : "A non directional promoter motif with consensus CGMYGYCR.",
-          "xrefs" : [ "PMID:16827941" ]
+          "val" : "A tRNA sequence that has a proline anticodon, and a 3' proline binding region.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "NDM2 motif",
+          "val" : "prolyl tRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non directional promoter motif 2",
+          "val" : "prolyl-transfer RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "NDM2",
+          "val" : "prolyl-transfer ribonucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48477,118 +52444,97 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "NDM2_motif"
+      "lbl" : "prolyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002010",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001599",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid.",
+          "val" : "A sequence variant that changes the resulting polypeptide structure.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pyrrolysine loss",
+          "val" : "3D polypeptide structure variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-24T02:30:16Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Request from  Uma Devi Paila, UVA.  Variants in the sites of rare amino acids e.g. Selenocysteine.  These are important impact terms since a loss of such rare amino acids may lead to a loss of function."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:44:46Z"
+        } ]
       },
       "type" : "CLASS",
-      "lbl" : "pyrrolysine_loss"
+      "lbl" : "3D_polypeptide_structure_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001162",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001115",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).",
-          "xrefs" : [ "PMID:12537576:15231738", "PMID:16858867" ]
+          "val" : "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "motif ten element",
+          "pred" : "hasRelatedSynonym",
+          "val" : "helix-l",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "motif_ten_element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "CSARCSSAACGS",
+          "val" : "left handed helix",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00222"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "MTE"
+      "lbl" : "left_handed_peptide_helix"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001161",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001114",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).",
-          "xrefs" : [ "PMID:12537576:16827941" ]
+          "val" : "A helix is a secondary_structure conformation where the peptide backbone forms a coil.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "DMv2 motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "MKSYGGCARCGSYSS",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "promoter motif 8",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "DMv2",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "directional motif v2",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "helix",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00152"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DMv2_motif"
+      "lbl" : "peptide_helix"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002011",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001598",
       "meta" : {
         "definition" : {
-          "val" : "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping  sequence.",
+          "val" : "A sequence variant within the transcript that changes the structure of the translational product.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:INTRAGENIC",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:intragenic_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "intragenic variant",
+          "val" : "translational product structure variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48596,39 +52542,32 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-24T02:33:13Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Pablo Cingolani, for use in SnpEff."
+          "val" : "2010-03-22T02:44:17Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intragenic_variant"
+      "lbl" : "translational_product_structure_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001164",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000267",
       "meta" : {
         "definition" : {
-          "val" : "A promoter motif with consensus sequence CGGACGT.",
-          "xrefs" : [ "PMID:16827941" ]
+          "val" : "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "directional motif 5",
+          "val" : "phenylalanyl-transfer ribonucleic acid",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DMp5",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "directional promoter motif 5",
+          "val" : "phenylalanyl tRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DPE1 motif",
+          "val" : "phenylalanyl-transfer RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48637,64 +52576,107 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DPE1_motif"
+      "lbl" : "phenylalanyl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001163",
+      "id" : "http://purl.obolibrary.org/obo/so#processed_into",
       "meta" : {
         "definition" : {
-          "val" : "A promoter motif with consensus sequence TCATTCG.",
-          "xrefs" : [ "PMID:16827941" ]
+          "val" : "X is processed_into Y if a region X is modified to create Y.",
+          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INR1 motif",
-          "xrefs" : [ ]
+        "comments" : [ "Example: miRNA_primary_transcript processed into miRNA." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "directional motif p3",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-08-19T12:15:02Z"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "DMp3",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "processed_into"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001117",
+      "meta" : {
+        "definition" : {
+          "val" : "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier.",
+          "xrefs" : [ "EBIBS:GAR" ]
+        },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Alpha_helix"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "a-helix",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "directional promoter motif 3",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "helix",
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00040"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "INR1_motif"
+      "lbl" : "alpha_helix"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001160",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001116",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).",
-          "xrefs" : [ "PMID:12537576:16827941" ]
+          "val" : "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DMv3",
+          "val" : "right handed helix",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "KNNCAKCNCTRNY",
-          "xrefs" : [ ]
+          "pred" : "hasRelatedSynonym",
+          "val" : "helix",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:0000339"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "right_handed_peptide_helix"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000269",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has a serine anticodon, and a 3' serine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "promoter motif 7",
+          "val" : "seryl tRNA",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "DMv3 motif",
+          "pred" : "hasRelatedSynonym",
+          "val" : "seryl-transfer ribonucleic acid",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "directional motif v3",
+          "val" : "seryl-transfer RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48703,61 +52685,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DMv3_motif"
+      "lbl" : "seryl_tRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002009",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002003",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby at least one base of a codon encoding selenocysteine  is changed, resulting in a different encoded amino acid.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR).",
+          "xrefs" : [ "SGD:jd" ]
         },
+        "comments" : [ "Requested by Janos Demeter, SGD." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "selenocysteine loss",
+          "val" : "Z2-segment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-24T02:29:44Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Request from  Uma Devi Paila, UVA.  Variants in the sites of rare amino acids e.g. Selenocysteine.  These are important impact terms since a loss of such rare amino acids may lead to a loss of function."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-01-05T07:36:45Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "selenocysteine_loss"
+      "lbl" : "Z2_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001159",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001155",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).",
-          "xrefs" : [ "PMID:12537576:16827941" ]
+          "val" : "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees.",
+          "xrefs" : [ "PMID:2371257", "SO:cb" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "promoter motif 6",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "DMv5",
+          "val" : "type VIII turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "directional motif v5",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "KTYRGTATWTTT",
+          "val" : "type VIII beta turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DMv5 motif",
+          "val" : "beta turn type eight",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48766,97 +52739,94 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DMv5_motif"
+      "lbl" : "beta_turn_type_eight"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002007",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002004",
       "meta" : {
         "definition" : {
-          "val" : "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS.",
+          "xrefs" : [ "SGD:jd" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "multiple nucleotide substitution",
+          "val" : "ARS consensus sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "multiple nucleotide variant",
+          "val" : "ACS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-13T03:48:40Z"
+          "val" : "2014-01-05T07:47:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "MNV"
+      "lbl" : "ARS_consensus_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002008",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001154",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees.",
+          "xrefs" : [ "PMID:2371257", "SO:cb" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:rare_amino_acid_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "type VIb turn",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:RARE_AMINO_ACID",
+          "val" : "type VIb beta turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "rare amino acid variant",
+          "val" : "beta turn type six b",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Request from  Uma Devi Paila, UVA.  Variants in the sites of rare amino acids e.g. Selenocysteine.  These are important impact terms since a loss of such rare amino acids may lead to a loss of function."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-03-24T02:24:01Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rare_amino_acid_variant"
+      "lbl" : "beta_turn_type_six_b"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001158",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001157",
       "meta" : {
         "definition" : {
-          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).",
-          "xrefs" : [ "PMID:12537576:16827941" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014).",
+          "xrefs" : [ "PMID:16827941:12537576" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "E box motif",
+          "val" : "promoter motif 1",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "NDM5",
+          "pred" : "hasNarrowSynonym",
+          "val" : "YGGTCACATR",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "AWCAGCTGWT",
+          "pred" : "hasExactSynonym",
+          "val" : "motif 1 element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "generic E box motif",
+          "val" : "directional motif v4",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DMv4",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DMv4 motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48865,77 +52835,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "E_box_motif"
+      "lbl" : "DMv4_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002005",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002001",
       "meta" : {
         "definition" : {
-          "val" : "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome.",
-          "xrefs" : [ "PMID:22645662" ]
+          "val" : "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha).",
+          "xrefs" : [ "SGD:jd" ]
         },
+        "comments" : [ "Requested by Janos Demeter, SGD." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DSR motif",
+          "val" : "Y-region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:51:27Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Antonia Locke, (Pombe)."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-01-05T07:33:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DSR_motif"
+      "lbl" : "Y_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002006",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001156",
       "meta" : {
         "definition" : {
-          "val" : "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc.",
-          "xrefs" : [ "PMID:24003116", "POMBE:mh" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW.",
+          "xrefs" : [ "PMID:12537576" ]
         },
+        "comments" : [ "This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "zinc repressed element",
+          "val" : "WATCGATW_motif",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T09:23:27Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "zinc_repressed_element"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001199",
-      "meta" : {
-        "definition" : {
-          "val" : "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ss RNA viral sequence",
+          "val" : "NDM4",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "single strand RNA virus",
+          "val" : "DRE motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -48944,79 +52889,84 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ss_RNA_viral_sequence"
+      "lbl" : "DRE_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002047",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002002",
       "meta" : {
         "definition" : {
-          "val" : "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli.",
-          "xrefs" : [ "PMID:24789973", "SO:ke" ]
+          "val" : "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR).",
+          "xrefs" : [ "SGD:jd" ]
         },
+        "comments" : [ "Requested by Janos Demeter, SGD." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcription pause site",
+          "val" : "Z1-region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-01-05T07:34:59Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-02-09T15:32:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcription_pause_site"
+      "lbl" : "Z1_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002048",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001151",
       "meta" : {
         "definition" : {
-          "val" : "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).",
-          "xrefs" : [ "SGD:se" ]
+          "val" : "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees.",
+          "xrefs" : [ "PMID:2371257", "SO:cb" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "disabled ORF",
+          "val" : "type VIa beta turn",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "disabled_reading frame",
+          "pred" : "hasExactSynonym",
+          "val" : "type VIa turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "dORF",
+          "val" : "beta turn type six a",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-02-09T16:15:46Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "disabled_reading_frame"
+      "lbl" : "beta_turn_type_six_a"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001198",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001150",
       "meta" : {
         "definition" : {
-          "val" : "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline.",
+          "xrefs" : [ "SO:cb" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "double stranded DNA virus",
+          "val" : "type VI beta turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ds DNA viral sequence",
+          "val" : "cis-proline loop",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "beta turn type six",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "type VI turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -49025,289 +52975,312 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ds_DNA_viral_sequence"
+      "lbl" : "beta_turn_type_six"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002045",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002000",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0002024"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001153",
       "meta" : {
         "definition" : {
-          "val" : "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].",
-          "xrefs" : [ "PMID:1489142", "SO:ke" ]
+          "val" : "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees.",
+          "xrefs" : [ "PMID:27428516" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "PRE",
+          "val" : "type VIa2 turn",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "pheromone response element",
+          "val" : "beta turn type six a two",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "type VIa2 beta turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Rama, SGD."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-02-09T15:05:43Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pheromone_response_element"
+      "lbl" : "beta_turn_type_six_a_two"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002046",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001152",
       "meta" : {
         "definition" : {
-          "val" : "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae.",
-          "xrefs" : [ "PMID:1489142", "SO:ke" ]
+          "val" : "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees.",
+          "xrefs" : [ "PMID:27428516" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "filamentation and invasion response element",
+          "val" : "type VIa1 turn",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "beta turn type six a one",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "type VIa1 beta turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Rama, SGD."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-02-09T15:09:47Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "FRE"
+      "lbl" : "beta_turn_type_six_a_one"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002043",
+      "id" : "http://purl.obolibrary.org/obo/so#lost",
       "meta" : {
         "definition" : {
-          "val" : "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
+          "val" : "X lost Y if X is a variant_of X' and Y part of X' but not X.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "miR encoding Y-RNA primary transcript",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:37:46Z"
+          "val" : "2011-06-28T12:53:16Z"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "miR_encoding_Y_RNA_primary_transcript"
+      "type" : "PROPERTY",
+      "lbl" : "lost"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001195",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001148",
       "meta" : {
         "definition" : {
-          "val" : "An oligo composed of (R)-GNA residues.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "Site which has been experimentally altered.",
+          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Discrete." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "(R)-glycol nucleic acid",
-          "xrefs" : [ ]
+          "val" : "mutagen",
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "R GNA oligo",
+          "val" : "mutated_site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "(R)-glycerol nucleic acid",
+          "val" : "mutagenesis",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00036"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "R_GNA_oligo"
+      "lbl" : "mutated_variant_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002044",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001147",
       "meta" : {
         "definition" : {
-          "val" : "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT.",
-          "xrefs" : [ "PMID:1489142", "PMID:20118212", "SO:ke" ]
+          "val" : "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars.",
+          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Discrete." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "TEA Consensus Sequence ",
+          "pred" : "hasBroadSynonym",
+          "val" : "natural_variant",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "TCS element",
+          "pred" : "hasBroadSynonym",
+          "val" : "variant",
+          "xrefs" : [ "uniprot:feature_type" ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "sequence variation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Rama - SGD."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-02-09T15:02:53Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00071"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TCS_element"
+      "lbl" : "natural_variant_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001194",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001149",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a GNA sequence in the (R)-GNA enantiomer.",
-          "xrefs" : [ "CHEBI:48016" ]
+          "val" : "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting.",
+          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
         },
+        "comments" : [ "Discrete." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "R GNA",
+          "val" : "alternative_sequence",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead."
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "R_GNA"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001197",
-      "meta" : {
-        "definition" : {
-          "val" : "An oligo composed of (S)-GNA residues.",
-          "xrefs" : [ "RSC:cb" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "(S)-glycerol nucleic acid",
+          "pred" : "hasNarrowSynonym",
+          "val" : "isoform",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "(S)-glycol nucleic acid",
+          "val" : "var_seq",
+          "xrefs" : [ "uniprot:feature_type" ]
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "varsplic",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "S GNA oligo",
+          "pred" : "hasNarrowSynonym",
+          "val" : "sequence variation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001065"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00073"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "S_GNA_oligo"
+      "lbl" : "alternate_sequence_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002041",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001144",
       "meta" : {
         "definition" : {
-          "val" : "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miR encoding vaultRNA primary transcript",
+          "val" : "st_turn_ir",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "st turn right handed type one",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:34:32Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00235"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miR_encoding_vaultRNA_primary_transcript"
+      "lbl" : "st_turn_right_handed_type_one"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002042",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000297",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a  Y-RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "comments" : [ "Moved from is_a: SO:0000296 origin_of_replication to is_a: SO:0001411 biological_region after Terrence Murphy (INSDC) pointed out that the D loop can also refer to a loop in DNA repair, which is not an origin of replication. See GitHub Issue #417 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/417)" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/D_loop"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Y-RNA primary transcript",
+          "val" : "D-loop",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:36:51Z"
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:D-loop",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "displacement loop",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Y_RNA_primary_transcript"
+      "lbl" : "D_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001196",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001143",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a GNA sequence in the (S)-GNA enantiomer.",
-          "xrefs" : [ "CHEBI:48017" ]
+          "val" : "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "S GNA",
+          "val" : "st_turn_iil",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "st turn left handed type two",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00232"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "S_GNA"
+      "lbl" : "st_turn_left_handed_type_two"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001191",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000296",
       "meta" : {
         "definition" : {
-          "val" : "An oligo composed of TNA residues.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites.",
+          "xrefs" : [ "NCBI:cf", "http://www.insdc.org/files/feature_table.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Threose_nucleic_acid"
+          "val" : "http://en.wikipedia.org/wiki/Origin_of_replication"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TNA oligo",
+          "val" : "INSDC_feature:rep_origin",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "threose nucleic acid",
+          "val" : "origin of replication",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ori",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -49316,293 +53289,261 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TNA_oligo"
+      "lbl" : "origin_of_replication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001190",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000299",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.",
-          "xrefs" : [ "CHEBI:48019" ]
+          "val" : "A location where recombination or occurs during mitosis or meiosis.",
+          "xrefs" : [ ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "specific recombination site",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TNA"
+      "lbl" : "specific_recombination_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002040",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001146",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a  vaultRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis.",
+          "xrefs" : [ "EBIBS:GAR", "SO:ke" ]
         },
+        "comments" : [ "For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vaultRNA primary transcript",
+          "val" : "sequence_variations",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:33:33Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00336"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vaultRNA_primary_transcript"
+      "lbl" : "polypeptide_variation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001193",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001145",
       "meta" : {
         "definition" : {
-          "val" : "An oligo composed of GNA residues.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Glycerol_nucleic_acid"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "glycol nucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "GNA oligo",
+          "val" : "st turn right handed type two",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "glycerol nucleic acid",
+          "val" : "st_turn_iir",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "GNA_oligo"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001192",
-      "meta" : {
-        "definition" : {
-          "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.",
-          "xrefs" : [ "CHEBI:48015" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00233"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "GNA"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#edited_to",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T02:19:11Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "edited_to"
+      "lbl" : "st_turn_right_handed_type_two"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002038",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000298",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding an shRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A feature where there has been exchange of genetic material in the event of mitosis or meiosis",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "shRNA primary transcript",
+          "val" : "INSDC_qualifier:other",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "recombination feature",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_recomb",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:30:43Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "shRNA_primary_transcript"
+      "lbl" : "recombination_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002039",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000293",
       "meta" : {
         "definition" : {
-          "val" : "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A repetitive element that is engineered and foreign.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miR encoding shRNA primary transcript",
+          "val" : "engineered foreign repetitive element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:32:00Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miR_encoding_shRNA_primary_transcript"
+      "lbl" : "engineered_foreign_repetitive_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002036",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001140",
       "meta" : {
         "definition" : {
-          "val" : "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miR encoding lncRNA primary transcript",
+          "val" : "gamma turn inverse",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00221"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:23:48Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miR_encoding_lncRNA_primary_transcript"
+      "lbl" : "gamma_turn_inverse"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001188",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000292",
       "meta" : {
-        "definition" : {
-          "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.",
-          "xrefs" : [ "CHEBI:48010" ]
-        },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "LNA"
+      "lbl" : "repetitive_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001187",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000295",
       "meta" : {
         "definition" : {
-          "val" : "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.",
-          "xrefs" : [ "GOC:mah", "PMID:12457565" ]
+          "val" : "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs.",
+          "xrefs" : [ "PMID:9428511" ]
         },
+        "comments" : [ "May have either GT-AC or AT-AC 5' and 3' boundaries." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pseudouridylation guide snoRNA",
+          "val" : "U12 intron",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "U12-dependent intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Has RNA pseudouridylation guide activity (GO:0030558)."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudouridylation_guide_snoRNA"
+      "lbl" : "U12_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002037",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001142",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miR encoding tRNA primary transcript",
+          "val" : "st_turn_il",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "st turn left handed type one",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:28:23Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00234"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miR_encoding_tRNA_primary_transcript"
+      "lbl" : "st_turn_left_handed_type_one"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002034",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001141",
       "meta" : {
         "definition" : {
-          "val" : "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2).",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "miR encoding snoRNA primary transcript",
+          "val" : "serine/threonine turn",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "st_turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:02:13Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00231"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miR_encoding_snoRNA_primary_transcript"
+      "lbl" : "serine_threonine_turn"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001189",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000294",
       "meta" : {
         "definition" : {
-          "val" : "An oligo composed of LNA residues.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Locked_nucleic_acid"
+          "val" : "http://en.wikipedia.org/wiki/Inverted_repeat"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "LNA oligo",
+          "val" : "inverted repeat sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "locked nucleic acid",
+          "val" : "INSDC_qualifier:inverted",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "inverted repeat",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -49611,273 +53552,272 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "LNA_oligo"
+      "lbl" : "inverted_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002035",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000291",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a  lncRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a repeating trinucleotide sequence (three bases).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lncRNA primary transcript",
+          "val" : "trinucleotide repeat microsatellite feature",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "rinucleotide repeat microsatellite",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "trinucleotide repeat microsatellite locus",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "dinucleotide repeat microsatellite marker",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T15:23:03Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lncRNA_primary_transcript"
+      "lbl" : "trinucleotide_repeat_microsatellite_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002032",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000290",
       "meta" : {
         "definition" : {
-          "val" : "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a repeating dinucleotide sequence (two bases).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "microRNA-offset RNA",
+          "val" : "dinucleotide repeat microsatellite marker",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T13:57:43Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "hasExactSynonym",
+          "val" : "dinucleotide repeat microsatellite",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015."
+          "pred" : "hasExactSynonym",
+          "val" : "dinucleotide repeat microsatellite locus",
+          "xrefs" : [ ]
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "moR"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001184",
-      "meta" : {
-        "definition" : {
-          "val" : "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.",
-          "xrefs" : [ "RSC:cb" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "peptide nucleic acid",
+          "pred" : "hasExactSynonym",
+          "val" : "dinucleotide repeat microsatellite feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "PNA"
+      "lbl" : "dinucleotide_repeat_microsatellite_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002033",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001137",
       "meta" : {
         "definition" : {
-          "val" : "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "loop-origin miRs",
+          "val" : "beta_turn_iir",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "type II turn",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "beta turn right handed type two",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "type II beta turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-01-09T14:02:02Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00214"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "loR"
+      "lbl" : "beta_turn_right_handed_type_two"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001183",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000289",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem.",
+          "xrefs" : [ "NCBI:th", "http://www.informatics.jax.org/silver/glossary.shtml" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Morpholino"
+          "val" : "http://en.wikipedia.org/wiki/Microsatellite"
         } ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "morpholino backbone",
+          "val" : "INSDC_qualifier:microsatellite",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead."
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "morpholino_backbone"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001186",
-      "meta" : {
-        "definition" : {
-          "val" : "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.",
-          "xrefs" : [ "RSC:cb" ]
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this for feature annotation. Use ribozyme (SO:0000374) instead."
+          "pred" : "hasExactSynonym",
+          "val" : "microsatellite locus",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "short tandem repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "microsatellite marker",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "STR",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9651/" ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ribozymic"
+      "lbl" : "microsatellite"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002030",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001136",
       "meta" : {
         "definition" : {
-          "val" : "One of two segments of homology found at all three mating loci (HML, MAT and HMR).",
-          "xrefs" : [ "SGD:jd" ]
+          "val" : "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "x-region",
+          "val" : "type I beta turn",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "beta_turn_ir",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "type I turn",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "beta turn right handed type one",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-07-14T18:43:21Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00216"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "X_region"
+      "lbl" : "beta_turn_right_handed_type_one"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001185",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001139",
       "meta" : {
         "definition" : {
-          "val" : "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.",
-          "xrefs" : [ "RSC:cb" ]
+          "val" : "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "gamma turn classic",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "classic gamma turn",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00220"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "enzymatic"
+      "lbl" : "gamma_turn_classic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002031",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001138",
       "meta" : {
         "definition" : {
-          "val" : "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference.",
-          "xrefs" : [ "PMID:6699500", "SO:ke" ]
+          "val" : "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http:en.wikipedia.org/wiki/Small_hairpin_RNA"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "small hairpin RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "short hairpin RNA",
+          "val" : "gamma turn",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00219"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-10-23T09:16:29Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "shRNA"
+      "lbl" : "gamma_turn"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001180",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002025",
       "meta" : {
         "definition" : {
-          "val" : "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.",
-          "xrefs" : [ "PMID:7892223" ]
+          "val" : "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I.",
+          "xrefs" : [ "PMID:22582262", "PMID:23117617", "PMID:24173580", "PomBase:vw" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/AU-rich_element"
-        } ],
+        "comments" : [ "Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the \"Mei2 dot\". This term was Requested by Val Wood, PomBase." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "AU-rich element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ARE",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "AU rich element",
+          "val" : "cis-acting homologous chromosome pairing region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-07-14T11:40:34Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "AU_rich_element"
+      "lbl" : "cis_acting_homologous_chromosome_pairing_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001182",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001177",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.",
-          "xrefs" : [ "PMID:3198610", "PMID:8710843" ]
+          "val" : "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C.",
+          "xrefs" : [ "ISBN:0716719207" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Iron_responsive_element"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "IRE",
+          "val" : "TpsiC loop",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "iron responsive element",
+          "val" : "T loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -49886,132 +53826,128 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "iron_responsive_element"
+      "lbl" : "T_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001181",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002026",
       "meta" : {
         "definition" : {
-          "val" : "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.",
-          "xrefs" : [ "PMID:10893231" ]
+          "val" : "The nucleotide sequence which encodes the intein portion of the precursor gene.",
+          "xrefs" : [ "PMID:8165123" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "BRE",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Bruno response element",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Requested by Janos Demeter 2014." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-07-14T11:53:21Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Bruno_response_element"
+      "lbl" : "intein_encoding_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002029",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001176",
       "meta" : {
         "definition" : {
-          "val" : "A translated ORF encoded entirely within the antisense strand of a known protein coding gene.",
-          "xrefs" : [ "POMBASE:vw" ]
+          "val" : "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues.",
+          "xrefs" : [ "ISBN:071671920" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translated nested antisense gene",
+          "val" : "DHU loop",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "D loop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-07-14T12:04:32Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tnaORF"
+      "lbl" : "DHU_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002027",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001179",
       "meta" : {
         "definition" : {
-          "val" : "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation.",
-          "xrefs" : [ "PMID:12890013", "PMID:16153175", "POMBASE:mah" ]
+          "val" : "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012" ]
         },
+        "comments" : [ "The definition is most of the old definition for snoRNA (SO:0000275)." ],
         "xrefs" : [ {
-          "val" : "PMID:26684391"
+          "val" : "http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "upstream ORF",
+          "val" : "U3 small nucleolar RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "regulatory uORF",
+          "val" : "U3 snoRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snoRNA U3",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small nucleolar RNA U3",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-07-14T11:59:23Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "uORF"
+      "lbl" : "U3_snoRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002028",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002023",
       "meta" : {
         "definition" : {
-          "val" : "An open reading frame that encodes a peptide of less than 100 amino acids.",
-          "xrefs" : [ "PMID:23970561", "PMID:24705786", "POMBASE:mah" ]
+          "val" : "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library.",
+          "xrefs" : [ "OBO:prs", "PMID:22574170" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "small ORF",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "smORF",
+          "val" : "multiplexing sequence identifier",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-05-30T15:13:16Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-07-14T12:02:33Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sORF"
+      "lbl" : "multiplexing_sequence_identifier"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002069",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002024",
       "meta" : {
         "definition" : {
-          "val" : "A deletion of a LINE1 mobile element with respect to a reference.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR.",
+          "xrefs" : [ "SGD:jd" ]
         },
+        "comments" : [ "MERGED COMMENT:\nTARGET COMMENT: Requested by Janos Demeter, SGD.\n--------------------\nSOURCE COMMENT: Requested by Janos Demeter, SGD." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "LINE1 deletion",
+          "pred" : "hasExactSynonym",
+          "val" : "W-region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0002000"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
@@ -50019,231 +53955,244 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-09-04T13:46:26Z"
+          "val" : "2014-07-11T13:20:08Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "LINE1_deletion"
+      "lbl" : "W_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002067",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001178",
       "meta" : {
         "definition" : {
-          "val" : "A deletion of the HERV mobile element with respect to  a reference.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "A primary transcript encoding pyrrolysyl tRNA (SO:0000766).",
+          "xrefs" : [ "RSC:cb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "HERV deletion",
+          "val" : "pyrrolysine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-09-04T13:42:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "HERV_deletion"
+      "lbl" : "pyrrolysine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002068",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002021",
       "meta" : {
         "definition" : {
-          "val" : "A deletion of an SVA mobile element.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.",
+          "xrefs" : [ "PMID:17614787" ]
         },
+        "comments" : [ "Requested by Midori Harris." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SVA deletion",
+          "val" : "mating type region replication fork barrier",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-09-04T13:45:22Z"
+          "val" : "2014-05-30T14:57:26Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SVA_deletion"
+      "lbl" : "mating_type_region_replication_fork_barrier"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002065",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001173",
       "meta" : {
         "definition" : {
-          "val" : "An insertion of sequence from the SVA family of mobile elements.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3.",
+          "xrefs" : [ "ISBN:0716719207" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-06-18T11:36:12Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "anticodon loop",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "anti-codon loop",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SVA_insertion"
+      "lbl" : "anticodon_loop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002066",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002022",
       "meta" : {
         "definition" : {
-          "val" : "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element).",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts.",
+          "xrefs" : [ "PMID:20178743", "PMID:24095277", "PomBase:al" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mobile element deletion",
+          "val" : "primal small RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-05-30T15:01:24Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-09-04T13:40:43Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mobile_element_deletion"
+      "lbl" : "priRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002063",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001172",
       "meta" : {
         "definition" : {
-          "val" : "An insertion of sequence from the Alu family of mobile elements.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "A region of a tRNA.",
+          "xrefs" : [ "RSC:cb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Alu insertion",
+          "val" : "tRNA region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-06-18T11:30:36Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Alu_insertion"
+      "lbl" : "tRNA_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002064",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001175",
       "meta" : {
         "definition" : {
-          "val" : "An insertion from the Line1 family of mobile elements.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid.",
+          "xrefs" : [ "ISBN:0716719207" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "line1 insertion",
+          "pred" : "hasExactSynonym",
+          "val" : "CCA tail",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CCA sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-06-18T11:34:44Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "LINE1_insertion"
+      "lbl" : "CCA_tail"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002061",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002020",
       "meta" : {
         "definition" : {
-          "val" : "A translocation where the regions involved are from the same chromosome.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions.",
+          "xrefs" : [ "PMID:24013502" ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+        "comments" : [ "Requested by Antonia Lock. Insulator is included as a related synonym since this is used to refer to insulator in the literature (NCBI:cf)." ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "insulator",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "boundary element",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-06-18T11:10:51Z"
+          "val" : "2014-05-30T14:45:37Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intrachromosomal_translocation"
+      "lbl" : "boundary_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002062",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001174",
       "meta" : {
         "definition" : {
-          "val" : "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA.",
+          "xrefs" : [ "RSC:cb" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Anticodon"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "complex chromosomal rearrangement",
+          "val" : "anti-codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-06-18T11:24:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "complex_chromosomal_rearrangement"
+      "lbl" : "anticodon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002060",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001171",
       "meta" : {
         "definition" : {
-          "val" : "A translocation where the regions involved are from different chromosomes.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "A component of the large ribosomal subunit in mitochondrial rRNA.",
+          "xrefs" : [ "RSC:cb" ]
         },
+        "comments" : [ "This term has been merged into mt_LSU_rRNA (SO:0002345) as part of reorganization of rRNA child terms 10 June 2021. Requested by EBI. See GitHub Issue #493." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "rRNA 21S",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "21S LSU rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "21S rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "21S ribosomal RNA",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-06-18T11:10:30Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0002345"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "interchromosomal_translocation"
+      "lbl" : "rRNA_21S"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001192",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001170",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements.",
+          "xrefs" : [ "PMID:16537396" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "encodes disjoint polypeptides",
+          "pred" : "hasRelatedSynonym",
+          "val" : "maverick element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -50252,36 +54201,60 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_disjoint_polypeptides"
+      "lbl" : "polinton"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001191",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002018",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons.",
+          "val" : "A transcript variant occurring within a conserved region of an intron.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Uma Paila (UVA) for snpEff." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "encodes overlapping peptides different start",
+          "val" : "snpEff:INTRON_CONSERVED",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "conserved intron variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:conserved_intron_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-25T02:58:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_overlapping_peptides_different_start"
+      "lbl" : "conserved_intron_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001190",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001169",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons.",
+          "val" : "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "encodes different polypeptides different stop",
+          "val" : "double stranded RNA virus sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ds RNA viral sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -50290,349 +54263,392 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_different_polypeptides_different_stop"
+      "lbl" : "ds_RNA_viral_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001196",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002019",
       "meta" : {
         "definition" : {
-          "val" : "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A sequence variant where at least one base in the start codon is changed, but the start remains.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:SYNONYMOUS_START",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-28T10:08:41Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cryptogene"
+      "lbl" : "start_retained_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001195",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002016",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences.",
+          "val" : "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "encodes overlapping peptides",
+          "val" : "3 prime UTR elongation",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "encodes_overlapping_peptides"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#integral_part_of",
-      "meta" : {
-        "definition" : {
-          "val" : "X integral_part_of Y if and only if: X part_of Y and Y has_part X.",
-          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T12:03:28Z"
+          "val" : "2014-03-25T10:55:33Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: exon integral_part_of transcript."
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "integral_part_of"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001194",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping"
+      "lbl" : "3_prime_UTR_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001193",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002017",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons.",
+          "val" : "A sequence variant located in a conserved intergenic region, between genes.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Uma Paila (UVA) for snpEff." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "encodes overlapping polypeptides different start and stop",
+          "val" : "snpEff:INTERGENIC_CONSERVED",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:conserved_intergenic_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "conserved intergenic variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-25T02:54:39Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_overlapping_polypeptides_different_start_and_stop"
+      "lbl" : "conserved_intergenic_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001197",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002014",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript that has the quality dicistronic.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "dicistronic primary transcript",
+          "val" : "5 prime UTR elongation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-25T10:48:26Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dicistronic_primary_transcript"
+      "lbl" : "5_prime_UTR_elongation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002058",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001166",
       "meta" : {
         "definition" : {
-          "val" : "An exonic  splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.",
-          "xrefs" : [ "PMID:23241926", "SO:ke" ]
+          "val" : "A non directional promoter motif with consensus sequence GAGAGCG.",
+          "xrefs" : [ "PMID:16827941" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "exonic splicing silencer",
+          "val" : "NDM1",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ESS",
+          "val" : "GAGA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "GAGA motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Javier Diez Perez."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T12:42:12Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exonic_splicing_silencer"
+      "lbl" : "GAGA_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002059",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002015",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory_region that promotes or induces the process of recombination.",
-          "xrefs" : [ "PMID:8861911", "SGD:se" ]
+          "val" : "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "recombination enhancer",
+          "val" : "snpEff:UTR_3_DELETED",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:3_prime_utr_truncation",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "3 prime UTR truncation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T13:08:58Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-25T10:54:50Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombination_enhancer"
+      "lbl" : "3_prime_UTR_truncation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002056",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001165",
       "meta" : {
         "definition" : {
-          "val" : "An intronic  splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.",
-          "xrefs" : [ "PMID:23241926", "SO:ke" ]
+          "val" : "A promoter motif with consensus sequence CARCCCT.",
+          "xrefs" : [ "PMID:16827941" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "ISS",
+          "pred" : "hasRelatedSynonym",
+          "val" : "DMv1",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "intronic splicing silencer",
+          "val" : "DMv1 motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "directional promoter motif v1",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Javier Diez Perez."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T12:24:10Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intronic_splicing_silencer"
+      "lbl" : "DMv1_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002057",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001168",
       "meta" : {
+        "definition" : {
+          "val" : "A non directional promoter motif with consensus sequence GAAAGCT.",
+          "xrefs" : [ "PMID:16827941" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ISE",
+          "val" : "non directional motif 3",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T12:28:31Z"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "hasExactSynonym",
+          "val" : "NDM3",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "NDM3 motif",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intronic_splicing_enhancer"
+      "lbl" : "NDM3_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002054",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002012",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby the gene product has diminished or abolished function.",
+          "val" : "A codon variant that changes at least one base of the canonical start codon.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "loss of function variant",
-          "xrefs" : [ ]
+          "val" : "VEP:start_lost",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:start_lost",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:START_LOST",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-24T02:41:28Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T11:21:29Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "loss_of_function_variant"
+      "lbl" : "start_lost"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002055",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002013",
       "meta" : {
         "definition" : {
-          "val" : "A variant whereby the gene product is not functional or the gene product is not produced.",
+          "val" : "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "null mutation",
+          "val" : "snpEff:UTR_5_DELETED",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5 prime UTR truncation",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:5_prime_utr_truncation",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T11:21:57Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-25T10:46:42Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "null_mutation"
+      "lbl" : "5_prime_UTR_truncation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002052",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001167",
       "meta" : {
         "definition" : {
-          "val" : "A variant where the mutated gene product adversely affects the other (wild type) gene product.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non directional promoter motif with consensus CGMYGYCR.",
+          "xrefs" : [ "PMID:16827941" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "dominant negative variant",
+          "val" : "non directional promoter motif 2",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "dominant negative",
+          "val" : "NDM2 motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "NDM2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Deanna Church."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T11:16:28Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dominant_negative_variant"
+      "lbl" : "NDM2_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002053",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001162",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby new or enhanced function is conferred on the gene product.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159).",
+          "xrefs" : [ "PMID:12537576:15231738", "PMID:16858867" ]
         },
         "synonyms" : [ {
+          "pred" : "hasNarrowSynonym",
+          "val" : "CSARCSSAACGS",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "gain of function variant",
+          "val" : "motif_ten_element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "motif ten element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T11:20:47Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gain_of_function_variant"
+      "lbl" : "MTE"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002050",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002010",
       "meta" : {
         "definition" : {
-          "val" : "A promoter that allows for continual transcription of gene.",
+          "val" : "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "constitutive promoter",
+          "val" : "pyrrolysine loss",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T10:39:09Z"
+          "val" : "2014-03-24T02:30:16Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -50642,17 +54658,31 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "constitutive_promoter"
+      "lbl" : "pyrrolysine_loss"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002051",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002011",
       "meta" : {
         "definition" : {
-          "val" : "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors.",
+          "val" : "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Pablo Cingolani, for use in SnpEff." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inducible promoter",
+          "val" : "snpEff:INTRAGENIC",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:intragenic_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "intragenic variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -50663,21 +54693,37 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T10:39:56Z"
+          "val" : "2014-03-24T02:33:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inducible_promoter"
+      "lbl" : "intragenic_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001189",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001161",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).",
+          "xrefs" : [ "PMID:12537576:16827941" ]
         },
         "synonyms" : [ {
+          "pred" : "hasNarrowSynonym",
+          "val" : "MKSYGGCARCGSYSS",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "encodes greater than 1 polypeptide",
+          "val" : "DMv2 motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "promoter motif 8",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "directional motif v2",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DMv2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -50686,17 +54732,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_greater_than_1_polypeptide"
+      "lbl" : "DMv2_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001188",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001164",
       "meta" : {
         "definition" : {
-          "val" : "A gene that is alternately spliced, but encodes only one polypeptide.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A promoter motif with consensus sequence CGGACGT.",
+          "xrefs" : [ "PMID:16827941" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "encodes 1 polypeptide",
+          "val" : "DPE1 motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "directional motif 5",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DMp5",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "directional promoter motif 5",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -50705,49 +54763,64 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "encodes_1_polypeptide"
+      "lbl" : "DPE1_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002049",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001163",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated.",
-          "xrefs" : [ "SO:rs" ]
+          "val" : "A promoter motif with consensus sequence TCATTCG.",
+          "xrefs" : [ "PMID:16827941" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K27ac",
+          "val" : "INR1 motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K27 acetylation site",
+          "val" : "directional promoter motif 3",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by: Sagar Jain, Richard Scheuermann."
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-05-14T10:17:11Z"
+          "pred" : "hasExactSynonym",
+          "val" : "DMp3",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "directional motif p3",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K27_acetylation_site"
+      "lbl" : "INR1_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001187",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001160",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that is alternatively spliced.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162).",
+          "xrefs" : [ "PMID:12537576:16827941" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "alternatively spliced transcript",
+          "val" : "DMv3 motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "promoter motif 7",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DMv3",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "KNNCAKCNCTRNY",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "directional motif v3",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -50756,99 +54829,126 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alternatively_spliced_transcript"
+      "lbl" : "DMv3_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_1001186",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002009",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence variant causing cryptic splice acceptor activation",
+          "val" : "selenocysteine loss",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
-          "val" : "SO:0001570"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-03-24T02:29:44Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_variant_causing_cryptic_splice_acceptor_activation"
+      "lbl" : "selenocysteine_loss"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#exemplar_of",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001159",
       "meta" : {
         "definition" : {
-          "val" : "X is exemplar of Y if X is the best evidence for Y.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162).",
+          "xrefs" : [ "PMID:12537576:16827941" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "promoter motif 6",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DMv5",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "directional motif v5",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DMv5 motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasNarrowSynonym",
+          "val" : "KTYRGTATWTTT",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Tracker id: 2594157."
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "exemplar_of"
+      "type" : "CLASS",
+      "lbl" : "DMv5_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002089",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002007",
       "meta" : {
         "definition" : {
-          "val" : "A UTR variant of exonic sequence of the 3' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence.",
+          "xrefs" : [ "NCBI:th" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3 prime UTR exon variant",
+          "val" : "multiple nucleotide substitution",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "multiple nucleotide variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by visze github tracker ID 346."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-03-07T10:37:04Z"
+          "val" : "2014-01-13T03:48:40Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "3_prime_UTR_exon_variant"
+      "lbl" : "MNV"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002087",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002008",
       "meta" : {
         "definition" : {
-          "val" : "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene.",
+          "val" : "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "pseudogenic CDS",
+          "val" : "rare amino acid variant",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:CDS",
-          "xrefs" : [ ]
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:rare_amino_acid_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:pseudo",
-          "xrefs" : [ ]
+          "val" : "snpEff:RARE_AMINO_ACID",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-02-29T12:58:52Z"
+          "val" : "2014-03-24T02:24:01Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -50858,134 +54958,124 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "pseudogenic_CDS"
+      "lbl" : "rare_amino_acid_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002088",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001158",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015).",
+          "xrefs" : [ "PMID:12537576:16827941" ]
         },
         "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "generic E box motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "E box motif",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasNarrowSynonym",
-          "val" : "ANNOVAR:ncRNA_splicing",
+          "val" : "AWCAGCTGWT",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "NDM5",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-03-07T09:40:46Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_coding_transcript_splice_region_variant"
+      "lbl" : "E_box_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002085",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002005",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby two genes, on the same strand have become joined.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome.",
+          "xrefs" : [ "PMID:22645662" ]
         },
+        "comments" : [ "Requested by Antonia Locke, (Pombe)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unidirectional gene fusion",
+          "val" : "DSR motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by SNPEFF team. Feb 2016."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-02-23T12:16:48Z"
+          "val" : "2014-01-05T07:51:27Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unidirectional_gene_fusion"
+      "lbl" : "DSR_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002086",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002006",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby two genes, on alternate strands have become joined.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc.",
+          "xrefs" : [ "PMID:24003116", "POMBE:mh" ]
         },
+        "comments" : [ "This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bidirectional gene fusion",
+          "val" : "zinc repressed element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by SNPEFF team. Feb 2016."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-02-23T12:17:18Z"
+          "val" : "2014-01-05T09:23:27Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bidirectional_gene_fusion"
+      "lbl" : "zinc_repressed_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002083",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001199",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located within 2KB 3' of a gene.",
+          "val" : "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:near-gene-3",
+          "val" : "ss RNA viral sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "single strand RNA virus",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-24T15:55:49Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "2KB_downstream_variant"
+      "lbl" : "ss_RNA_viral_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002084",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002047",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli.",
+          "xrefs" : [ "PMID:24789973", "SO:ke" ]
         },
+        "comments" : [ "Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:coding-near-splice",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:exonic;splicing",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "exonic splice region variant",
+          "val" : "transcription pause site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -50993,72 +55083,60 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-12-01T14:38:47Z"
+          "val" : "2015-02-09T15:32:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exonic_splice_region_variant"
+      "lbl" : "transcription_pause_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002081",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001198",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects the coding regions of an incompletely annotated transcript.",
+          "val" : "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:coding-unknown",
+          "val" : "double stranded DNA virus",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:coding-notMod3",
+          "val" : "ds DNA viral sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-24T15:32:27Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_CDS"
+      "lbl" : "ds_DNA_viral_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002082",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002048",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons).",
+          "xrefs" : [ "SGD:se" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:coding-unknown-near-splice",
+          "val" : "dORF",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "incomplete transcript coding splice variant",
+          "pred" : "hasRelatedSynonym",
+          "val" : "disabled_reading frame",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:coding-notMod3-near-splice",
+          "val" : "disabled ORF",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-24T15:51:06Z"
+          "val" : "2015-02-09T16:15:46Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -51068,100 +55146,101 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_coding_splice_variant"
+      "lbl" : "disabled_reading_frame"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002080",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002045",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects the exon of an incompletely annotated transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)].",
+          "xrefs" : [ "PMID:1489142", "SO:ke" ]
         },
+        "comments" : [ "Requested by Rama, SGD." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "incomplete transcript exonic variant",
+          "val" : "pheromone response element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "PRE",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-24T12:52:10Z"
+          "val" : "2015-02-09T15:05:43Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_exonic_variant"
+      "lbl" : "pheromone_response_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002078",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002046",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects the intron of an incompletely annotated transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae.",
+          "xrefs" : [ "PMID:1489142", "SO:ke" ]
         },
+        "comments" : [ "Requested by Rama, SGD." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "incomplete transcript intronic variant",
+          "val" : "filamentation and invasion response element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-24T12:51:45Z"
+          "val" : "2015-02-09T15:09:47Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_intronic_variant"
+      "lbl" : "FRE"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002079",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001195",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects the splice region of an incompletely annotated transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An oligo composed of (R)-GNA residues.",
+          "xrefs" : [ "RSC:cb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "incomplete transcript splice region variant",
+          "val" : "(R)-glycerol nucleic acid",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-24T12:52:06Z"
+          "pred" : "hasExactSynonym",
+          "val" : "R GNA oligo",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "(R)-glycol nucleic acid",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_splice_region_variant"
+      "lbl" : "R_GNA_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002076",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002043",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects the 3' UTR of an incompletely annotated transcript.",
+          "val" : "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "incomplete transcript 3UTR variant",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:ncRNA_UTR3",
-          "xrefs" : [ "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/" ]
+          "val" : "miR encoding Y-RNA primary transcript",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -51171,117 +55250,124 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-23T14:45:52Z"
+          "val" : "2015-01-09T15:37:46Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_3UTR_variant"
+      "lbl" : "miR_encoding_Y_RNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002077",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001194",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects the 5' UTR of an incompletely annotated transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An attribute describing a GNA sequence in the (R)-GNA enantiomer.",
+          "xrefs" : [ "CHEBI:48016" ]
         },
-        "xrefs" : [ {
-          "val" : "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/"
+        "comments" : [ "Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "R GNA",
+          "xrefs" : [ ]
         } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "R_GNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002044",
+      "meta" : {
+        "definition" : {
+          "val" : "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT.",
+          "xrefs" : [ "PMID:1489142", "PMID:20118212", "SO:ke" ]
+        },
+        "comments" : [ "Requested by Rama - SGD." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "incomplete transcript 5UTR variant",
+          "val" : "TEA Consensus Sequence ",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:ncRNA_UTR5",
-          "xrefs" : [ "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/" ]
+          "val" : "TCS element",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-24T12:39:17Z"
+          "val" : "2015-02-09T15:02:53Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_5UTR_variant"
+      "lbl" : "TCS_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002074",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001197",
       "meta" : {
         "definition" : {
-          "val" : "A variant that falls in an intergenic region that is 1 kb or less between 2 genes.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An oligo composed of (S)-GNA residues.",
+          "xrefs" : [ "RSC:cb" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:upstream;downstream",
+          "val" : "S GNA oligo",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "(S)-glycol nucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "(S)-glycerol nucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is added to map to the Annovar annotation 'upstream,downstream' ."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-23T14:24:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intergenic_1kb_variant"
+      "lbl" : "S_GNA_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002075",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002041",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that intersects an incompletely annotated transcript.",
+          "val" : "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "incomplete transcript variant",
+          "val" : "miR encoding vaultRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-23T14:43:51Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation.  \n\nIt is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:34:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "incomplete_transcript_variant"
+      "lbl" : "miR_encoding_vaultRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100020",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001196",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA.",
-          "xrefs" : [ "EBIBS:GAR", "SO:ke" ]
+          "val" : "An attribute describing a GNA sequence in the (S)-GNA enantiomer.",
+          "xrefs" : [ "CHEBI:48017" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DNA_bind",
-          "xrefs" : [ "uniprot:feature" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "polypeptide DNA contact",
+          "val" : "S GNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -51290,79 +55376,119 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_DNA_contact"
+      "lbl" : "S_GNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002072",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002042",
       "meta" : {
         "definition" : {
-          "val" : "A position or feature where two sequences have been compared.",
-          "xrefs" : [ ]
+          "val" : "A primary transcript encoding a Y-RNA.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence comparison",
+          "val" : "Y-RNA primary transcript",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_feature",
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:36:51Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "Y_RNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001191",
+      "meta" : {
+        "definition" : {
+          "val" : "An oligo composed of TNA residues.",
+          "xrefs" : [ "RSC:cb" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Threose_nucleic_acid"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "threose nucleic acid",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:sequence_comparison",
+          "val" : "TNA oligo",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-23T14:14:32Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_comparison"
+      "lbl" : "TNA_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002073",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002040",
       "meta" : {
         "definition" : {
-          "val" : "A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence.",
+          "val" : "A primary transcript encoding a vaultRNA.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "no sequence alteration",
+          "val" : "vaultRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is requested by the ClinVar data model group for use in the allele registry and such. A sequence at a defined location that is defined to match the reference assembly."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-11-23T14:15:08Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:33:33Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "no_sequence_alteration"
+      "lbl" : "vaultRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100021",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001190",
       "meta" : {
         "definition" : {
-          "val" : "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone.",
+          "xrefs" : [ "CHEBI:48019" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "TNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001193",
+      "meta" : {
+        "definition" : {
+          "val" : "An oligo composed of GNA residues.",
+          "xrefs" : [ "RSC:cb" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Glycerol_nucleic_acid"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide conserved region",
+          "val" : "glycol nucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "GNA oligo",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "glycerol nucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -51371,154 +55497,164 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_conserved_region"
+      "lbl" : "GNA_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002070",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001192",
       "meta" : {
         "definition" : {
-          "val" : "A deletion of an Alu mobile element with respect to a reference.",
-          "xrefs" : [ "NCBI:th" ]
+          "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA.",
+          "xrefs" : [ "CHEBI:48015" ]
         },
+        "comments" : [ "Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "GNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#edited_to",
+      "meta" : {
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-08-19T02:19:11Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-09-04T13:47:16Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "Alu_deletion"
+      "type" : "PROPERTY",
+      "lbl" : "edited_to"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002071",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002038",
       "meta" : {
         "definition" : {
-          "val" : "A CDS that is supported by proteomics data.",
+          "val" : "A primary transcript encoding an shRNA.",
           "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "shRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2015-10-12T13:25:02Z"
+          "val" : "2015-01-09T15:30:43Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CDS_supported_by_peptide_spectrum_match"
+      "lbl" : "shRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100017",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002039",
       "meta" : {
         "definition" : {
-          "val" : "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "motif",
+          "pred" : "hasExactSynonym",
+          "val" : "miR encoding shRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:32:00Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_conserved_motif"
+      "lbl" : "miR_encoding_shRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100018",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002036",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide binding motif",
+          "val" : "miR encoding lncRNA primary transcript",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "binding",
-          "xrefs" : [ "uniprot:feature_type" ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:23:48Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_binding_motif"
+      "lbl" : "miR_encoding_lncRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100015",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001188",
       "meta" : {
         "definition" : {
-          "val" : "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link.",
+          "xrefs" : [ "CHEBI:48010" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "C-region",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "c_terminal_region"
+      "lbl" : "LNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100016",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002037",
       "meta" : {
         "definition" : {
-          "val" : "The central, hydrophobic region of the signal peptide (approx 7-15 aa).",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "central hydrophobic region of signal peptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "H-region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "central_hydrophobic_region",
+          "val" : "miR encoding tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:28:23Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "central_hydrophobic_region_of_signal_peptide"
+      "lbl" : "miR_encoding_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100019",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001187",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue.",
+          "xrefs" : [ "GOC:mah", "PMID:12457565" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Has RNA pseudouridylation guide activity (GO:0030558)." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "catalytic_motif",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide catalytic motif",
+          "val" : "pseudouridylation guide snoRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -51527,73 +55663,74 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_catalytic_motif"
+      "lbl" : "pseudouridylation_guide_snoRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100010",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002034",
       "meta" : {
         "definition" : {
-          "val" : "An experimental region wherean analysis has been run and not produced any annotation.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "no output",
+          "val" : "miR encoding snoRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:02:13Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "no_output"
+      "lbl" : "miR_encoding_snoRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100013",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002035",
       "meta" : {
         "definition" : {
-          "val" : "Hydrophobic regions are regions with a low affinity for water.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A primary transcript encoding a lncRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "hydrophobic_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "hydrophobicity",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "hydropathic",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "hydrophobic region of peptide",
+          "val" : "lncRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T15:23:03Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "hydrophobic_region_of_peptide"
+      "lbl" : "lncRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100014",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001189",
       "meta" : {
         "definition" : {
-          "val" : "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An oligo composed of LNA residues.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Locked_nucleic_acid"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "N-region",
+          "pred" : "hasExactSynonym",
+          "val" : "LNA oligo",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "locked nucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -51602,49 +55739,44 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "n_terminal_region"
+      "lbl" : "LNA_oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100011",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002032",
       "meta" : {
         "definition" : {
-          "val" : "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens", "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cleaved peptide region",
+          "val" : "microRNA-offset RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T13:57:43Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cleaved_peptide_region"
+      "lbl" : "moR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100012",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001184",
       "meta" : {
         "definition" : {
-          "val" : "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "peptide coil",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "random coil",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "coil",
+          "val" : "peptide nucleic acid",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -51653,38 +55785,47 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "peptide_coil"
+      "lbl" : "PNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100006",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002033",
       "meta" : {
         "definition" : {
-          "val" : "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "catmat-3r",
+          "val" : "loop-origin miRs",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-01-09T14:02:02Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "catmat_right_handed_three"
+      "lbl" : "loR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100007",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001183",
       "meta" : {
         "definition" : {
-          "val" : "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Morpholino"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "catmat-4r",
+          "val" : "morpholino backbone",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -51693,86 +55834,115 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "catmat_right_handed_four"
+      "lbl" : "morpholino_backbone"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100004",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002030",
       "meta" : {
         "definition" : {
-          "val" : "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "One of two segments of homology found at all three mating loci (HML, MAT and HMR).",
+          "xrefs" : [ "SGD:jd" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "catmat-3l",
+          "val" : "x-region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-07-14T18:43:21Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "catmat_left_handed_three"
+      "lbl" : "X_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100005",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001186",
       "meta" : {
         "definition" : {
-          "val" : "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170.  The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "catmat-4l",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Do not use this for feature annotation. Use ribozyme (SO:0000374) instead." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "catmat_left_handed_four"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset",
-      "type" : "PROPERTY",
-      "lbl" : "in_subset"
+      "lbl" : "ribozymic"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100008",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002031",
       "meta" : {
         "definition" : {
-          "val" : "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference.",
+          "xrefs" : [ "PMID:6699500", "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http:http:en.wikipedia.org/wiki/Small_hairpin_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "alpha beta motif",
+          "val" : "small hairpin RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "short hairpin RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-10-23T09:16:29Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alpha_beta_motif"
+      "lbl" : "shRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100009",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001185",
       "meta" : {
         "definition" : {
-          "val" : "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein.",
+          "xrefs" : [ "RSC:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "enzymatic"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001180",
+      "meta" : {
+        "definition" : {
+          "val" : "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable.",
+          "xrefs" : [ "PMID:7892223" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/AU-rich_element"
+        } ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ARE",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "prokaryotic membrane lipoprotein lipid attachment site",
+          "val" : "AU-rich element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "lipoprotein signal peptide",
+          "val" : "AU rich element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -51781,226 +55951,203 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lipoprotein_signal_peptide"
+      "lbl" : "AU_rich_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002098",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001182",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogene derived from an immunoglobulin gene.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins.",
+          "xrefs" : [ "PMID:3198610", "PMID:8710843" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Iron_responsive_element"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "immunoglobulin pseudogene",
+          "val" : "iron responsive element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "IRE",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:01:47Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "immunoglobulin_pseudogene"
+      "lbl" : "iron_responsive_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002099",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001181",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogene derived from a T-cell receptor gene.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs.",
+          "xrefs" : [ "PMID:10893231" ]
         },
+        "comments" : [ "Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Bruno response element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "BRE",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:02:18Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "T_cell_receptor_pseudogene"
+      "lbl" : "Bruno_response_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002096",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002029",
       "meta" : {
         "definition" : {
-          "val" : "A variation that expands or contracts a tandem repeat with regard to a reference.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A translated ORF encoded entirely within the antisense strand of a known protein coding gene.",
+          "xrefs" : [ "POMBASE:vw" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "short tandem repeat variation",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "str variation",
+          "val" : "translated nested antisense gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-14T16:04:40Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2014-07-14T12:04:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "short_tandem_repeat_variation"
+      "lbl" : "tnaORF"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002097",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002027",
       "meta" : {
         "definition" : {
-          "val" : "A pseudogene derived from a vertebrate immune system gene.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation.",
+          "xrefs" : [ "PMID:12890013", "PMID:16153175", "POMBASE:mah" ]
         },
+        "xrefs" : [ {
+          "val" : "PMID:26684391"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "vertebrate immune system pseudogene",
+          "val" : "regulatory uORF",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "upstream ORF",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-07-14T11:59:23Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-07-15T16:00:22Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "vertebrate_immune_system_pseudogene"
+      "lbl" : "uORF"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002094",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002028",
       "meta" : {
         "definition" : {
-          "val" : "A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination.",
-          "xrefs" : [ ]
+          "val" : "An open reading frame that encodes a peptide of less than 100 amino acids.",
+          "xrefs" : [ "PMID:23970561", "PMID:24705786", "POMBASE:mah" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "NAHRR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non allelic homologous recombination region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:non_allelic_homologous_recombination",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_recomb",
+          "val" : "smORF",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:non_allelic_homologous",
+          "val" : "small ORF",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-05-17T13:34:12Z"
+          "val" : "2014-07-14T12:02:33Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_allelic_homologous_recombination_region"
+      "lbl" : "sORF"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002095",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002069",
       "meta" : {
         "definition" : {
-          "val" : "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs).",
-          "xrefs" : [ "PMC:126017", "SO:nrs" ]
+          "val" : "A deletion of a LINE1 mobile element with respect to a reference.",
+          "xrefs" : [ "NCBI:th" ]
         },
-        "xrefs" : [ {
-          "val" : "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "small Cajal body specific RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small Cajal body-specific RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "LINE1 deletion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-05-19T13:42:45Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "nicole"
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-09-04T13:46:26Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "scaRNA"
+      "lbl" : "LINE1_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002092",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002067",
       "meta" : {
         "definition" : {
-          "val" : "A UTR variant of exonic sequence of the 5' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A deletion of the HERV mobile element with respect to a reference.",
+          "xrefs" : [ "NCBI:th" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5 prime UTR exon variant",
+          "val" : "HERV deletion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by visze github tracker ID 346."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-09-04T13:42:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-03-07T10:38:26Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_exon_variant"
+      "lbl" : "HERV_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002093",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002068",
       "meta" : {
         "definition" : {
-          "val" : "A variant that impacts the internal interactions of the resulting polypeptide structure.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A deletion of an SVA mobile element.",
+          "xrefs" : [ "NCBI:th" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "structural interaction variant",
+          "val" : "SVA deletion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -52008,56 +56155,47 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-03-07T11:43:55Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Pablo Cingolani. The way I calculate this is simply by looking at the PDB entry of one protein and then marking those AA that are within 3 Angstrom of each  other (and far away in the AA sequence, e.g. over 20 AA distance). The assumption is that, since they are very close in distance, they  must be \"interacting\" and thus important for protein structure."
+          "val" : "2015-09-04T13:45:22Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "structural_interaction_variant"
+      "lbl" : "SVA_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100002",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002065",
       "meta" : {
         "definition" : {
-          "val" : "A region that is involved a contact with another molecule.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An insertion of sequence from the SVA family of mobile elements.",
+          "xrefs" : [ "NCBI:th" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "molecular contact region",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-06-18T11:36:12Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "molecular_contact_region"
+      "lbl" : "SVA_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002090",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002066",
       "meta" : {
         "definition" : {
-          "val" : "A UTR variant of intronic sequence of the 3' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element).",
+          "xrefs" : [ "NCBI:th" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "3 prime UTR intron variant",
+          "val" : "mobile element deletion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by visze github tracker ID 346."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
@@ -52065,504 +56203,326 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-03-07T10:37:41Z"
+          "val" : "2015-09-04T13:40:43Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "3_prime_UTR_intron_variant"
+      "lbl" : "mobile_element_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0002091",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002063",
       "meta" : {
         "definition" : {
-          "val" : "A UTR variant of intronic sequence of the 5' UTR.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An insertion of sequence from the Alu family of mobile elements.",
+          "xrefs" : [ "NCBI:th" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5 prime UTR intron variant",
+          "val" : "Alu insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by visze github tracker ID 346."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-06-18T11:30:36Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2016-03-07T10:38:04Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_intron_variant"
+      "lbl" : "Alu_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100003",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002064",
       "meta" : {
         "definition" : {
-          "val" : "A region of polypeptide chain with high conformational flexibility.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "An insertion from the Line1 family of mobile elements.",
+          "xrefs" : [ "NCBI:th" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "disordered region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "intrinsically unstructured polypeptide region",
+          "val" : "line1 insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-06-18T11:34:44Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intrinsically_unstructured_polypeptide_region"
+      "lbl" : "LINE1_insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0100001",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002061",
       "meta" : {
         "definition" : {
-          "val" : "A region of a peptide that is involved in a biochemical function.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A translocation where the regions involved are from the same chromosome.",
+          "xrefs" : [ "NCBI:th" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "biochemical motif",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "biochemical region of peptide",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "biochemical_region",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-06-18T11:10:51Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "biochemical_region_of_peptide"
+      "lbl" : "intrachromosomal_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001929",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002062",
       "meta" : {
         "definition" : {
-          "val" : "A sequencer read of a mitochondrial DNA sample.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis.",
+          "xrefs" : [ "NCBI:th" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mitochondrial DNA read",
+          "val" : "complex chromosomal rearrangement",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience, October, 2012."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-11-14T04:39:56Z"
+          "val" : "2015-06-18T11:24:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mitochondrial_DNA_read"
+      "lbl" : "complex_chromosomal_rearrangement"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001926",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002060",
       "meta" : {
         "definition" : {
-          "val" : "A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts are antisense of ARRET transcripts.",
-          "xrefs" : [ "PMID:22139915" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "anti-ARRET",
-          "xrefs" : [ ]
-        } ],
+          "val" : "A translocation where the regions involved are from different chromosomes.",
+          "xrefs" : [ "NCBI:th" ]
+        },
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-06-18T11:10:30Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T01:40:22Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "anti_ARRET"
+      "lbl" : "interchromosomal_translocation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001925",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001192",
       "meta" : {
         "definition" : {
-          "val" : "A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts consist of C rich repeats.",
-          "xrefs" : [ "PMID:22139915" ]
+          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "encodes disjoint polypeptides",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T01:24:37Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ARIA"
+      "lbl" : "encodes_disjoint_polypeptides"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001928",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001191",
       "meta" : {
         "definition" : {
-          "val" : "A duplication of the distal region of a chromosome.",
-          "xrefs" : [ "SO:bm" ]
+          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "distal duplication",
+          "val" : "encodes overlapping peptides different start",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is used by Complete Genomics in the structural variant analysis files."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T01:56:44Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "distal_duplication"
+      "lbl" : "encodes_overlapping_peptides_different_start"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001927",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001190",
       "meta" : {
         "definition" : {
-          "val" : "A non-coding transcript derived from the transcript of the telomere.",
-          "xrefs" : [ "PMID:22139915" ]
+          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "telomeric transcript",
+          "val" : "encodes different polypeptides different stop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T01:42:15Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "telomeric_transcript"
+      "lbl" : "encodes_different_polypeptides_different_stop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001922",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001196",
       "meta" : {
         "definition" : {
-          "val" : "A scaffold composed of mitochondrial contigs.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mitochondrial scaffold",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mitochondrial supercontig",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mitochondrial_scaffold",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T12:42:45Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mitochondrial_supercontig"
+      "lbl" : "cryptogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001921",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001195",
       "meta" : {
         "definition" : {
-          "val" : "A contig of mitochondria derived sequences.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mitochondrial contig",
+          "val" : "encodes overlapping peptides",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience, October, 2012."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T12:34:38Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mitochondrial_contig"
+      "lbl" : "encodes_overlapping_peptides"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001924",
+      "id" : "http://purl.obolibrary.org/obo/so#integral_part_of",
       "meta" : {
         "definition" : {
-          "val" : "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats.",
-          "xrefs" : [ "PMID:2139915" ]
+          "val" : "X integral_part_of Y if and only if: X part_of Y and Y has_part X.",
+          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
         },
+        "comments" : [ "Example: exon integral_part_of transcript." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T01:11:49Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012."
+          "val" : "2009-08-19T12:03:28Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "ARRET"
+      "type" : "PROPERTY",
+      "lbl" : "integral_part_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001923",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001194",
       "meta" : {
-        "definition" : {
-          "val" : "A non-coding RNA transcript, derived from the transcription of the telomere. These  transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long.",
-          "xrefs" : [ "PMID:22139915" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "telomeric repeat containing RNA",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Telomeric transcription has been documented in mammals, birds,  fish, plants and  yeast. Requested by Antonia Lock, October 2012."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-31T01:06:40Z"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "TERRA"
+      "lbl" : "alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001920",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001193",
       "meta" : {
         "definition" : {
-          "val" : "An adenine methylated at the 6 nitrogen.",
-          "xrefs" : [ "SO:rtapella" ]
+          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m-6A",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "6mA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "6-methyladenine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "6-mA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m6a",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N6-methyladenine",
+          "val" : "encodes overlapping polypeptides different start and stop",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-17T12:54:23Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "N6_methyladenine"
+      "lbl" : "encodes_overlapping_polypeptides_different_start_and_stop"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001919",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001197",
       "meta" : {
         "definition" : {
-          "val" : "A cytosine methylated at the 4 nitrogen.",
-          "xrefs" : [ "SO:rtapella" ]
+          "val" : "A primary transcript that has the quality dicistronic.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
-        }, {
-          "val" : "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "m-4C",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N4-methylcytosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "4-methylcytosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "4-mC",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N4 methylcytosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m4c",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "N4_methylcytosine",
+          "val" : "dicistronic primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-17T12:50:40Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "4_methylcytosine"
+      "lbl" : "dicistronic_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001918",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002058",
       "meta" : {
         "definition" : {
-          "val" : "A cytosine methylated at the 5 carbon.",
-          "xrefs" : [ "SO:rtapella" ]
+          "val" : "An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.",
+          "xrefs" : [ "PMID:23241926", "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
-        }, {
-          "val" : "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2"
-        } ],
+        "comments" : [ "Requested by Javier Diez Perez." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5 methylcytosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5-mC",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "m-5C",
+          "val" : "ESS",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "m5c",
+          "val" : "exonic splicing silencer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-17T12:46:10Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2015-05-14T12:42:12Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_methylcytosine"
+      "lbl" : "exonic_splicing_silencer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001915",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002059",
       "meta" : {
         "definition" : {
-          "val" : "A region defined by a cluster of experimentally determined transcription starting sites.",
-          "xrefs" : [ "PMID:19624849", "PMID:21372179", "SO:andrewgibson" ]
+          "val" : "A regulatory_region that promotes or induces the process of recombination.",
+          "xrefs" : [ "PMID:8861911", "SGD:se" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "TSC",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "transcriptional start site cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "TSS cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "transcriptional initiation cluster",
+          "val" : "recombination enhancer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -52573,267 +56533,241 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-17T12:09:50Z"
+          "val" : "2015-05-14T13:08:58Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcription_start_cluster"
+      "lbl" : "recombination_enhancer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001914",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002056",
       "meta" : {
         "definition" : {
-          "val" : "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.",
-          "xrefs" : [ "PMID:14645529" ]
+          "val" : "An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control.",
+          "xrefs" : [ "PMID:23241926", "SO:ke" ]
         },
+        "comments" : [ "Requested by Javier Diez Perez." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DNA spacer replication fork barrier",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RTS1 element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "rDNA replication fork barrier",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "RFB",
+          "val" : "intronic splicing silencer",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "RTS1 barrier",
+          "val" : "ISS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Midori - June 2012."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-06-11T02:55:02Z"
+          "val" : "2015-05-14T12:24:10Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rDNA_replication_fork_barrier"
+      "lbl" : "intronic_splicing_silencer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001917",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002057",
       "meta" : {
-        "definition" : {
-          "val" : "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region.",
-          "xrefs" : [ "PMID:16645617", "SO:andrewgibson" ]
-        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_note:CAGE_cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "CAGE cluster",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_feature",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "CAGE_peak",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "CAGE peak",
+          "val" : "ISE",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-05-14T12:28:31Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-17T12:42:03Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "CAGE_cluster"
+      "lbl" : "intronic_splicing_enhancer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001916",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002054",
       "meta" : {
         "definition" : {
-          "val" : "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites.",
-          "xrefs" : [ "SO:andrewgibson" ]
+          "val" : "A sequence variant whereby the gene product has diminished or abolished function.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CAGE tag",
+          "val" : "loss of function variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-10-17T12:36:58Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2015-05-14T11:21:29Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CAGE_tag"
+      "lbl" : "loss_of_function_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001911",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002055",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where copies of a feature are increased relative to the reference.",
+          "val" : "A variant whereby the gene product is not functional or the gene product is not produced.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "copy number increase",
+          "val" : "null mutation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-13T11:26:32Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-05-14T11:21:57Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "copy_number_increase"
+      "lbl" : "null_mutation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001910",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002052",
       "meta" : {
         "definition" : {
-          "val" : "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature.",
+          "val" : "A variant where the mutated gene product adversely affects the other (wild type) gene product.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Deanna Church." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:frameshift deletion",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "frameshift truncation",
+          "val" : "dominant negative",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:frameshift_truncation",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "dominant negative variant",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-12T05:10:45Z"
+          "val" : "2015-05-14T11:16:28Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "frameshift_truncation"
+      "lbl" : "dominant_negative_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001913",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002053",
       "meta" : {
         "definition" : {
-          "val" : "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation.",
-          "xrefs" : [ "Invitrogen:kc" ]
+          "val" : "A sequence variant whereby new or enhanced function is conferred on the gene product.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bacterial RNApol promoter sigma ecf ",
+          "val" : "gain of function variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Kevin Clancy - invitrogen -May 2012."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-06-11T02:41:33Z"
+          "val" : "2015-05-14T11:20:47Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bacterial_RNApol_promoter_sigma_ecf"
+      "lbl" : "gain_of_function_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001912",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002050",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where copies of a feature are decreased relative to the reference.",
+          "val" : "A promoter that allows for continual transcription of gene.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "copy number decrease",
+          "val" : "constitutive promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-04-13T11:27:52Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2015-05-14T10:39:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "copy_number_decrease"
+      "lbl" : "constitutive_promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001948",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100042",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000569"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0002051",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3R2 dimethylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H3R2me2",
+          "val" : "inducible promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:59:17Z"
+          "val" : "2015-05-14T10:39:56Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3R2_dimethylation_site"
+      "lbl" : "inducible_promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000617",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001189",
       "meta" : {
+        "definition" : {
+          "val" : "A gene that is alternately spliced, and encodes more than one polypeptide.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNApol III promoter type 1",
+          "val" : "encodes greater than 1 polypeptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -52842,95 +56776,41 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNApol_III_promoter_type_1"
+      "lbl" : "encodes_greater_than_1_polypeptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001947",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001188",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A gene that is alternately spliced, but encodes only one polypeptide.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3R2 monomethylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : " H3R2me1",
+          "val" : "encodes 1 polypeptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:57:13Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3R2_monomethylation_site"
+      "lbl" : "encodes_1_polypeptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000616",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002049",
       "meta" : {
         "definition" : {
-          "val" : "The base where transcription ends.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "xrefs" : [ "SO:rs" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "Requested by: Sagar Jain, Richard Scheuermann." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcription end site",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "transcription_end_site"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000619",
-      "meta" : {
-        "definition" : {
-          "val" : "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/A-box"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "A-box",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Binds TFIIIC."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "A_box"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001949",
-      "meta" : {
-        "definition" : {
-          "val" : "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated.",
-          "xrefs" : [ "EBI:nj" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "H4R3 dimethylation site",
+          "val" : "H3K27ac",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H4R3me2",
+          "val" : "H3K27 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -52941,21 +56821,21 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T11:01:27Z"
+          "val" : "2015-05-14T10:17:11Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4R3_dimethylation_site"
+      "lbl" : "H3K27_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000618",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001187",
       "meta" : {
+        "definition" : {
+          "val" : "A transcript that is alternatively spliced.",
+          "xrefs" : [ "SO:xp" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "tRNA promoter",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "RNApol III promoter type 2",
+          "val" : "alternatively spliced transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -52964,493 +56844,529 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNApol_III_promoter_type_2"
+      "lbl" : "alternatively_spliced_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001944",
+      "id" : "http://purl.obolibrary.org/obo/so#exemplar_of",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "X is exemplar of Y if X is the best evidence for Y.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "H2AK9 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2AK9ac",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Tracker id: 2594157." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:48:11Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "H2AK9_acetylation_site"
+      "type" : "PROPERTY",
+      "lbl" : "exemplar_of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000613",
+      "id" : "http://purl.obolibrary.org/obo/SO_1001186",
       "meta" : {
-        "definition" : {
-          "val" : "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.",
-          "xrefs" : [ "SO:ke" ]
-        },
+        "comments" : [ "OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bacterial RNApol promoter",
+          "val" : "sequence variant causing cryptic splice acceptor activation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "SO:0001570"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "bacterial_RNApol_promoter"
+      "lbl" : "sequence_variant_causing_cryptic_splice_acceptor_activation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000612",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002089",
       "meta" : {
         "definition" : {
-          "val" : "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.",
-          "xrefs" : [ "http://nar.oupjournals.org/cgi/content/full/25/4/888" ]
+          "val" : "A UTR variant of exonic sequence of the 3' UTR.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Polypyrimidine_tract"
-        } ],
+        "comments" : [ "Requested by visze github tracker ID 346." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypyrimidine tract",
+          "val" : "3 prime UTR exon variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-03-07T10:37:04Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypyrimidine_tract"
+      "lbl" : "3_prime_UTR_exon_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001943",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002087",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A non functional descendant of the coding portion of a coding transcript, part of a pseudogene.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:CDS",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K4ac",
+          "val" : "pseudogenic CDS",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K4 acetylation site",
+          "val" : "INSDC_qualifier:pseudo",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:46:32Z"
+          "val" : "2016-02-29T12:58:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K4_acetylation_site"
+      "lbl" : "pseudogenic_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000615",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002088",
       "meta" : {
         "definition" : {
-          "val" : "A terminator signal for RNA polymerase III transcription.",
+          "val" : "A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "terminator of type 2 RNApol III promoter",
+          "pred" : "hasNarrowSynonym",
+          "val" : "ANNOVAR:ncRNA_splicing",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-03-07T09:40:46Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "terminator_of_type_2_RNApol_III_promoter"
+      "lbl" : "non_coding_transcript_splice_region_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001946",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002085",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A sequence variant whereby two genes, on the same strand have become joined.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by SNPEFF team. Feb 2016." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK15 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2BK15ac",
+          "val" : "unidirectional gene fusion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-02-23T12:16:48Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:53:23Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2BK15_acetylation_site"
+      "lbl" : "unidirectional_gene_fusion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001945",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002086",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A sequence variant whereby two genes, on alternate strands have become joined.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by SNPEFF team. Feb 2016." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K56 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K56ac",
+          "val" : "bidirectional gene fusion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:51:14Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2016-02-23T12:17:18Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K56_acetylation_site"
+      "lbl" : "bidirectional_gene_fusion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000614",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002083",
       "meta" : {
         "definition" : {
-          "val" : "A terminator signal for bacterial transcription.",
+          "val" : "A sequence variant located within 2KB 3' of a gene.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "bacterial terminator",
-          "xrefs" : [ ]
+          "val" : "Seattleseq:near-gene-3",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-11-24T15:55:49Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "bacterial_terminator"
+      "lbl" : "2KB_downstream_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001940",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002084",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj", "http://dx.doi.org/10.4161/epi.6.5.15623" ]
+          "val" : "A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK120ac",
-          "xrefs" : [ ]
+          "val" : "ANNOVAR:exonic;splicing",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "Seattleseq:coding-near-splice",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK120 acetylation site",
+          "val" : "exonic splice region variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:28:38Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-12-01T14:38:47Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2BK120_acetylation_site"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#dbsnp",
-      "type" : "PROPERTY",
-      "lbl" : "dbsnp variant terms"
+      "lbl" : "exonic_splice_region_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000611",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002081",
       "meta" : {
         "definition" : {
-          "val" : "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.",
+          "val" : "A sequence variant that intersects the coding regions of an incompletely annotated transcript.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "branch point",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "branch site",
-          "xrefs" : [ ]
+          "val" : "Seattleseq:coding-notMod3",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "branch_point",
-          "xrefs" : [ ]
+          "val" : "Seattleseq:coding-unknown",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-11-24T15:32:27Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "branch_site"
+      "lbl" : "incomplete_transcript_CDS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001942",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002082",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK20ac",
-          "xrefs" : [ ]
+          "val" : "Seattleseq:coding-notMod3-near-splice",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK20 acetylation site",
+          "val" : "Seattleseq:coding-unknown-near-splice",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "incomplete transcript coding splice variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-11-24T15:51:06Z"
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
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         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2BK20_acetylation_site"
+      "lbl" : "incomplete_transcript_coding_splice_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000610",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002080",
       "meta" : {
         "definition" : {
-          "val" : "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.",
+          "val" : "A sequence variant that intersects the exon of an incompletely annotated transcript.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polyA sequence",
+          "val" : "incomplete transcript exonic variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-11-24T12:52:10Z"
+        }, {
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+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polyA_sequence"
+      "lbl" : "incomplete_transcript_exonic_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001941",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002078",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A sequence variant that intersects the intron of an incompletely annotated transcript.",
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         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H4K91ac",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H4K91 acetylation site",
+          "val" : "incomplete transcript intronic variant",
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         } ],
         "basicPropertyValues" : [ {
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-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:41:04Z"
+          "val" : "2015-11-24T12:51:45Z"
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
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-      },
-      "type" : "CLASS",
-      "lbl" : "H4K91_acetylation_site"
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-      "meta" : {
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-          "val" : "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).",
-          "xrefs" : [ "http://www.rna.ucla.edu/" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "oligo U tail",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "oligo_U_tail"
+      "lbl" : "incomplete_transcript_intronic_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001937",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002079",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A sequence variant that intersects the splice region of an incompletely annotated transcript.",
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         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2BK12 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H2BK12ac",
+          "val" : "incomplete transcript splice region variant",
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         } ],
         "basicPropertyValues" : [ {
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:19:13Z"
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           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2BK12_acetylation_site"
+      "lbl" : "incomplete_transcript_splice_region_variant"
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-      "id" : "http://purl.obolibrary.org/obo/SO_0000606",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002076",
       "meta" : {
         "definition" : {
-          "val" : "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).",
-          "xrefs" : [ "http://dna.kdna.ucla.edu/rna/index.aspx" ]
+          "val" : "A sequence variant that intersects the 3' UTR of an incompletely annotated transcript.",
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         },
+        "xrefs" : [ {
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         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "editing domain",
+          "val" : "ANNOVAR:ncRNA_UTR3",
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+          "pred" : "hasRelatedSynonym",
+          "val" : "incomplete transcript 3UTR variant",
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         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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+          "val" : "2015-11-23T14:45:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "editing_domain"
+      "lbl" : "incomplete_transcript_3UTR_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000605",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002077",
       "meta" : {
         "definition" : {
-          "val" : "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.",
-          "xrefs" : [ "SO:cjm" ]
+          "val" : "A sequence variant that intersects the 5' UTR of an incompletely annotated transcript.",
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         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
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         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "intergenic region",
+          "val" : "ANNOVAR:ncRNA_UTR5",
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+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
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         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
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       },
       "type" : "CLASS",
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+      "lbl" : "incomplete_transcript_5UTR_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001936",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002074",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A variant that falls in an intergenic region that is 1 kb or less between 2 genes.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This term is added to map to the Annovar annotation 'upstream,downstream' ." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K36 acetylation site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "H3K36ac",
-          "xrefs" : [ ]
+          "val" : "ANNOVAR:upstream;downstream",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:16:55Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2015-11-23T14:24:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K36_acetylation_site"
+      "lbl" : "intergenic_1kb_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000608",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002075",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that intersects an incompletely annotated transcript.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This term is to map to the ANNOVAR term 'ncRNA' http://annovar.openbioinformatics.org/en/latest/user-guide/gene/ . The description in the documentation (11/23/15) 'variant overlaps a transcript without coding annotation in the gene definition'. and this is further clarified in the document: ncRNA above refers to RNA without coding annotation. It does not mean that this is a RNA that will never be translated; it merely means that the user-selected gene annotation system was not able to give a coding sequence annotation. It could still code protein products and may have such annotations in future versions of gene annotation or in another gene annotation system. For example, BC039000 is regarded as ncRNA by ANNOVAR when using UCSC Known Gene annotation, but it is regarded as a protein-coding gene by ANNOVAR when using ENSEMBL annotation.\n\nIt is further clarified in the comments section as: ncRNA does NOT mean conventional non-coding RNA. It means a RNA without complete coding sequence, and it can be a coding RNA that is annotated incorrectly by RefSeq or other gene definition systems." ],
+        "xrefs" : [ {
+          "val" : "http://annovar.openbioinformatics.org/en/latest/user-guide/gene/"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H ACA box snoRNA encoding",
+          "val" : "incomplete transcript variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-11-23T14:43:51Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H_ACA_box_snoRNA_encoding"
+      "lbl" : "incomplete_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001939",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002072",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A position or feature where two sequences have been compared.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H4K12 acetylation site",
+          "val" : "sequence comparison",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H4K12ac",
+          "val" : "INSDC_note:sequence_comparison",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -53461,50 +57377,47 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:26:15Z"
+          "val" : "2015-11-23T14:14:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4K12_acetylation_site"
+      "lbl" : "sequence_comparison"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001938",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100020",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA.",
+          "xrefs" : [ "EBIBS:GAR", "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H2AK5 acetylation site",
-          "xrefs" : [ ]
+          "val" : "DNA_bind",
+          "xrefs" : [ "uniprot:feature" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H2AK5ac",
+          "val" : "polypeptide DNA contact",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:20:57Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H2AK5_acetylation_site"
+      "lbl" : "polypeptide_DNA_contact"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000607",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100021",
       "meta" : {
         "definition" : {
-          "val" : "The region of an edited transcript that will not be edited.",
-          "xrefs" : [ "http://dna.kdna.ucla.edu/rna/index.aspx" ]
+          "val" : "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "unedited region",
+          "val" : "polypeptide conserved region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -53513,140 +57426,128 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "unedited_region"
+      "lbl" : "polypeptide_conserved_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001933",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002073",
       "meta" : {
         "definition" : {
-          "val" : "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end.",
+          "val" : "A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "This term is requested by the ClinVar data model group for use in the allele registry and such. A sequence at a defined location that is defined to match the reference assembly." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "restriction enzyme three prime single strand overhang",
+          "val" : "no sequence alteration",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T09:52:14Z"
+          "val" : "2015-11-23T14:15:08Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_three_prime_single_strand_overhang"
+      "lbl" : "no_sequence_alteration"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000602",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002070",
       "meta" : {
         "definition" : {
-          "val" : "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.",
-          "xrefs" : [ "http://www.rna.ucla.edu/index.html" ]
+          "val" : "A deletion of an Alu mobile element with respect to a reference.",
+          "xrefs" : [ "NCBI:th" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Guide_RNA"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "gRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:guide_RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "guide RNA",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-09-04T13:47:16Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "guide_RNA"
+      "lbl" : "Alu_deletion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001932",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002071",
       "meta" : {
         "definition" : {
-          "val" : "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end.",
+          "val" : "A CDS that is supported by proteomics data.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "restriction enzyme five prime single strand overhang",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2015-10-12T13:25:02Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T09:50:44Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_five_prime_single_strand_overhang"
+      "lbl" : "CDS_supported_by_peptide_spectrum_match"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000601",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100017",
       "meta" : {
+        "definition" : {
+          "val" : "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found.",
+          "xrefs" : [ "EBIBS:GAR" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "motif",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edited_by_G_addition"
+      "lbl" : "polypeptide_conserved_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001935",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100018",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "binding",
+          "xrefs" : [ "uniprot:feature_type" ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K20 trimethylation site",
+          "val" : "polypeptide binding motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T10:13:48Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K20_trimethylation_site"
+      "lbl" : "polypeptide_binding_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000604",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100015",
       "meta" : {
         "definition" : {
-          "val" : "Edited mRNA sequence mediated by a single guide RNA (SO:0000602).",
-          "xrefs" : [ "http://dna.kdna.ucla.edu/rna/index.aspx" ]
+          "val" : "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa).",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "editing block",
+          "pred" : "hasRelatedSynonym",
+          "val" : "C-region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -53655,141 +57556,145 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "editing_block"
+      "lbl" : "c_terminal_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001934",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100016",
       "meta" : {
         "definition" : {
-          "val" : "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The central, hydrophobic region of the signal peptide (approx 7-15 aa).",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "central_hydrophobic_region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "monomeric repeat",
+          "val" : "central hydrophobic region of signal peptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "H-region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T09:59:15Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "monomeric_repeat"
+      "lbl" : "central_hydrophobic_region_of_signal_peptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000603",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100019",
       "meta" : {
         "definition" : {
-          "val" : "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.",
-          "xrefs" : [ "http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml" ]
+          "val" : "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Group_II_intron"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "group II intron",
+          "val" : "polypeptide catalytic motif",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "catalytic_motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "GO:0000373."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "group_II_intron"
+      "lbl" : "polypeptide_catalytic_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000600",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100010",
       "meta" : {
+        "definition" : {
+          "val" : "An experimental region wherean analysis has been run and not produced any annotation.",
+          "xrefs" : [ "EBIBS:GAR" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "no output",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "edited_by_A_to_I_substitution"
+      "lbl" : "no_output"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001931",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100013",
       "meta" : {
         "definition" : {
-          "val" : "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "Hydrophobic regions are regions with a low affinity for water.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "consensus genomic DNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "hydrophobic region of peptide",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "hydropathic",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "hydrophobicity",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "consensus gDNA",
+          "val" : "hydrophobic_region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience November, 2012."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-11-28T12:53:14Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "consensus_gDNA"
+      "lbl" : "hydrophobic_region_of_peptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001930",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100014",
       "meta" : {
         "definition" : {
-          "val" : "A sequencer read of a chloroplast DNA sample.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa).",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "chloroplast DNA read",
+          "pred" : "hasRelatedSynonym",
+          "val" : "N-region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2012-11-14T04:43:45Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience, October, 2012."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chloroplast_DNA_read"
+      "lbl" : "n_terminal_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000640",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100011",
       "meta" : {
         "definition" : {
-          "val" : "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "external transcribed spacer region",
+          "val" : "cleaved peptide region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -53798,79 +57703,68 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "external_transcribed_spacer_region"
+      "lbl" : "cleaved_peptide_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001971",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100012",
       "meta" : {
+        "definition" : {
+          "val" : "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds).",
+          "xrefs" : [ "EBIBS:GAR" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "zinc_fing",
-          "xrefs" : [ "unirot:features" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "zinc finger binding site",
+          "val" : "peptide coil",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-29T04:41:53Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "hasRelatedSynonym",
+          "val" : "random coil",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "coil",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "zinc_finger_binding_site"
+      "lbl" : "peptide_coil"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001970",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100006",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant occurring within an intron of a non coding transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non coding transcript intron variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "Jannovar:non_coding_transcript_intron_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "ANNOVAR:ncRNA_intronic",
+          "val" : "catmat-3r",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-23T10:55:03Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_coding_transcript_intron_variant"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty",
-      "type" : "PROPERTY",
-      "lbl" : "synonym_type_property"
+      "lbl" : "catmat_right_handed_three"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000639",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100007",
       "meta" : {
         "definition" : {
-          "val" : "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "internal transcribed spacer region",
+          "val" : "catmat-4r",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -53879,17 +57773,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "internal_transcribed_spacer_region"
+      "lbl" : "catmat_right_handed_four"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000638",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100004",
       "meta" : {
         "definition" : {
-          "val" : "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.",
-          "xrefs" : [ "http://oregonstate.edu/instruction/bb492/general/glossary.html" ]
+          "val" : "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcribed spacer region",
+          "val" : "catmat-3l",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -53898,50 +57793,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcribed_spacer_region"
+      "lbl" : "catmat_left_handed_three"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001969",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100005",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant occurring within an intron of a coding transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:coding_transcript_intron_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "coding sequence intron variant",
+          "val" : "catmat-4l",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-23T10:54:17Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_transcript_intron_variant"
+      "lbl" : "catmat_left_handed_four"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000635",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#inSubset",
+      "type" : "PROPERTY",
+      "lbl" : "in_subset"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0100008",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript that donates the spliced leader to other mRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mini-exon donor RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "mini exon donor RNA",
+          "val" : "alpha beta motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -53950,265 +57837,244 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mini_exon_donor_RNA"
+      "lbl" : "alpha_beta_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001966",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100009",
       "meta" : {
         "definition" : {
-          "val" : "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
-        } ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5-carboxycytosine",
+          "val" : "prokaryotic membrane lipoprotein lipid attachment site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-caC",
+          "val" : "lipoprotein signal peptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-20T01:30:01Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_carboxylcytosine"
+      "lbl" : "lipoprotein_signal_peptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001965",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002098",
       "meta" : {
         "definition" : {
-          "val" : "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage.",
+          "val" : "A pseudogene derived from an immunoglobulin gene.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
-        } ],
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "8-oxoG",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "8-oxoguanine",
+          "val" : "immunoglobulin pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-20T01:27:51Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-15T16:01:47Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "8_oxoguanine"
+      "lbl" : "immunoglobulin_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000634",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002099",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA that encodes multiple proteins from at least two non-overlapping regions.",
-          "xrefs" : [ "SO:rd" ]
+          "val" : "A pseudogene derived from a T-cell receptor gene.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Polycistronic_mRNA"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "polycistronic processed transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "polycistronic mRNA",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-15T16:02:18Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polycistronic_mRNA"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#DBVAR",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "database of genomic structural variation"
-        } ]
-      },
-      "type" : "PROPERTY"
+      "lbl" : "T_cell_receptor_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001968",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002096",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant of a protein coding gene.",
+          "val" : "A variation that expands or contracts a tandem repeat with regard to a reference.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:coding_transcript_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "short tandem repeat variation",
+          "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "coding transcript variant",
+          "val" : "str variation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-22T04:34:49Z"
+          "val" : "2016-07-14T16:04:40Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_transcript_variant"
+      "lbl" : "short_tandem_repeat_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000637",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002097",
       "meta" : {
         "definition" : {
-          "val" : "A plasmid that is engineered.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A pseudogene derived from a vertebrate immune system gene.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "These terms have been requested by Adam Frankish to support Gencode and Vega biotypes. The terms are defined according to IGMT." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "engineered plasmid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "engineered plasmid gene",
+          "val" : "vertebrate immune system pseudogene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-07-15T16:00:22Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "engineered_plasmid"
+      "lbl" : "vertebrate_immune_system_pseudogene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000636",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002094",
       "meta" : {
+        "definition" : {
+          "val" : "A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "mini-exon",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:non_allelic_homologous",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_recomb",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "spliced leader RNA",
+          "val" : "NAHRR",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:non_allelic_homologous_recombination",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non allelic homologous recombination region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-05-17T13:34:12Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "nicole"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "spliced_leader_RNA"
+      "lbl" : "non_allelic_homologous_recombination_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001967",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002095",
       "meta" : {
         "definition" : {
-          "val" : "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs).",
+          "xrefs" : [ "PMC:126017", "PMID:27775477", "PMID:28869095", "SO:nrs" ]
         },
+        "comments" : [ "Moved from is_a ncRNA (SO:0000655) to is_a snoRNA (SO:0000275) as per request from FlyBase by Dave Sant 24 April 2021. See GitHub Issue #509." ],
         "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
+          "val" : "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126017/"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "8-oxoadenine",
+          "val" : "small Cajal body specific RNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "8-oxoA",
+          "val" : "small Cajal body-specific RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-20T01:31:05Z"
+          "val" : "2016-05-19T13:42:45Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "nicole"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "8_oxoadenine"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001962",
-      "meta" : {
-        "definition" : {
-          "val" : "A modified adenine DNA base feature.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-20T01:22:30Z"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "modified_adenine"
+      "lbl" : "scaRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000631",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002092",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding for more than one gene product.",
+          "val" : "A UTR variant of exonic sequence of the 5' UTR.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by visze github tracker ID 346." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polycistronic primary transcript",
+          "val" : "5 prime UTR exon variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2016-03-07T10:38:26Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polycistronic_primary_transcript"
+      "lbl" : "5_prime_UTR_exon_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001961",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002093",
       "meta" : {
         "definition" : {
-          "val" : "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon.",
+          "val" : "A variant that impacts the internal interactions of the resulting polypeptide structure.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
-        } ],
+        "comments" : [ "Requested by Pablo Cingolani. The way I calculate this is simply by looking at the PDB entry of one protein and then marking those AA that are within 3 Angstrom of each other (and far away in the AA sequence, e.g. over 20 AA distance). The assumption is that, since they are very close in distance, they must be \"interacting\" and thus important for protein structure." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5-formylcytosine",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5-fC",
+          "val" : "structural interaction variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -54216,24 +58082,26 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-17T05:06:13Z"
+          "val" : "2016-03-07T11:43:55Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_formylcytosine"
+      "lbl" : "structural_interaction_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000630",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100002",
       "meta" : {
         "definition" : {
-          "val" : "A start codon upstream of the ORF.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that is involved a contact with another molecule.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "upstream AUG codon",
+          "pred" : "hasRelatedSynonym",
+          "val" : "molecular contact region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -54242,43 +58110,23 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "upstream_AUG_codon"
+      "lbl" : "molecular_contact_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000633",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002090",
       "meta" : {
         "definition" : {
-          "val" : "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.",
-          "xrefs" : [ "SO:rd" ]
+          "val" : "A UTR variant of intronic sequence of the 3' UTR.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Monocistronic_mRNA"
-        } ],
+        "comments" : [ "Requested by visze github tracker ID 346." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "monocistronic processed transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "monocistronic mRNA",
+          "val" : "3 prime UTR intron variant",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "monocistronic_mRNA"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001964",
-      "meta" : {
-        "definition" : {
-          "val" : "A modified guanine DNA base feature.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-20T01:25:31Z"
+          "val" : "2016-03-07T10:37:41Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -54288,38 +58136,50 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_guanine"
+      "lbl" : "3_prime_UTR_intron_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001963",
+      "id" : "http://purl.obolibrary.org/obo/SO_0002091",
       "meta" : {
         "definition" : {
-          "val" : "A modified cytosine DNA base feature.",
+          "val" : "A UTR variant of intronic sequence of the 5' UTR.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by visze github tracker ID 346." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "5 prime UTR intron variant",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-20T01:23:47Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2016-03-07T10:38:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "modified_cytosine"
+      "lbl" : "5_prime_UTR_intron_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000632",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100003",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding for one gene product.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of polypeptide chain with high conformational flexibility.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "monocistronic primary transcript",
+          "val" : "intrinsically unstructured polypeptide region",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "disordered region",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -54327,388 +58187,474 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "monocistronic_primary_transcript"
+      "lbl" : "intrinsically_unstructured_polypeptide_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001960",
+      "id" : "http://purl.obolibrary.org/obo/SO_0100001",
       "meta" : {
         "definition" : {
-          "val" : "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a peptide that is involved in a biochemical function.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
-        "xrefs" : [ {
-          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
-        } ],
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "biochemical_region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-hmC",
+          "val" : "biochemical motif",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "5-hydroxymethylcytosine",
+          "val" : "biochemical region of peptide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-17T05:05:31Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_hydroxymethylcytosine"
+      "lbl" : "biochemical_region_of_peptide"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001959",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001929",
       "meta" : {
         "definition" : {
-          "val" : "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator.",
-          "xrefs" : [ "PMID:20801935", "SO:myl" ]
+          "val" : "A sequencer read of a mitochondrial DNA sample.",
+          "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience, October, 2012." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypyrimidine initiator",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "TCT element",
+          "val" : "mitochondrial DNA read",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-11-14T04:39:56Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-05-17T04:38:48Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TCT_motif"
+      "lbl" : "mitochondrial_DNA_read"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000628",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001926",
       "meta" : {
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "definition" : {
+          "val" : "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts.",
+          "xrefs" : [ "PMID:22139915" ]
+        },
+        "comments" : [ "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromosomal structural element",
+          "val" : "anti-ARRET",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-31T01:40:22Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_structural_element"
+      "lbl" : "anti_ARRET"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000627",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001925",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region that 1) when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region.",
-          "xrefs" : [ "NCBI:cf", "PMID:12154228", "SO:regcreative" ]
+          "val" : "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats.",
+          "xrefs" : [ "PMID:22139915" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Insulator_(genetics)"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:insulator",
-          "xrefs" : [ ]
+        "comments" : [ "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012." ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "insulator element",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-31T01:24:37Z"
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insulator"
+      "lbl" : "ARIA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001958",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001928",
       "meta" : {
         "definition" : {
-          "val" : "A kind of intron whereby the excision is driven by lariat formation.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A duplication of the distal region of a chromosome.",
+          "xrefs" : [ "SO:bm" ]
         },
+        "comments" : [ "This term is used by Complete Genomics in the structural variant analysis files." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lariat intron",
+          "val" : "distal duplication",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-07T10:58:40Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2012-10-31T01:56:44Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by PomBase 3604508."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lariat_intron"
+      "lbl" : "distal_duplication"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000629",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001927",
       "meta" : {
+        "definition" : {
+          "val" : "A non-coding transcript derived from the transcript of the telomere.",
+          "xrefs" : [ "PMID:22139915" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime open reading frame",
+          "val" : "telomeric transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-31T01:42:15Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_open_reading_frame"
+      "lbl" : "telomeric_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000624",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001922",
       "meta" : {
         "definition" : {
-          "val" : "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A scaffold composed of mitochondrial contigs.",
+          "xrefs" : [ "GMOD:ea" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Telomere"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "telomeric sequence",
+          "val" : "mitochondrial supercontig",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:telomere",
+          "val" : "mitochondrial scaffold",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "telomeric DNA",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "telomere"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001955",
-      "meta" : {
-        "definition" : {
-          "val" : "A polypeptide region that proves structure in a protein that affects the stability of the protein.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "protein stability element",
+          "val" : "mitochondrial_scaffold",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T03:32:47Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-31T12:42:45Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "protein_stability_element"
+      "lbl" : "mitochondrial_supercontig"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000623",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001921",
       "meta" : {
+        "definition" : {
+          "val" : "A contig of mitochondria derived sequences.",
+          "xrefs" : [ "GMOD:ea" ]
+        },
+        "comments" : [ "Requested by Bayer Cropscience, October, 2012." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA encoding",
+          "val" : "mitochondrial contig",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-31T12:34:38Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "snRNA_encoding"
+      "lbl" : "mitochondrial_contig"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001954",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001924",
       "meta" : {
         "definition" : {
-          "val" : "A region related to restriction enzyme function.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats.",
+          "xrefs" : [ "PMID:2139915" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "restriction enzyme region",
-          "xrefs" : [ ]
-        } ],
+        "comments" : [ "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012." ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Not a great term for annotation, but used to classify the various regions related to restriction enzymes."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-31T01:11:49Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T03:23:34Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_region"
+      "lbl" : "ARRET"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001957",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001923",
       "meta" : {
         "definition" : {
-          "val" : "RNA secondary structure that affects the stability of an RNA molecule.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long.",
+          "xrefs" : [ "PMID:22139915" ]
         },
+        "comments" : [ "Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012." ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "rna stability element",
+          "val" : "telomeric repeat containing RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T03:38:35Z"
+          "val" : "2012-10-31T01:06:40Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_stability_element"
+      "lbl" : "TERRA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000626",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001920",
       "meta" : {
+        "definition" : {
+          "val" : "An adenine methylated at the 6 nitrogen.",
+          "xrefs" : [ "SO:rtapella" ]
+        },
+        "xrefs" : [ {
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromosomal regulatory element",
+          "val" : "6-mA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "6mA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m-6A",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m6a",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N6-methyladenine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "6-methyladenine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-17T12:54:23Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_regulatory_element"
+      "lbl" : "N6_methyladenine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001956",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001919",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide_region that  codes for a protease cleavage site.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A cytosine methylated at the 4 nitrogen.",
+          "xrefs" : [ "SO:rtapella" ]
         },
+        "xrefs" : [ {
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
+        }, {
+          "val" : "http://www.insdc.org/files/feature_table.html#7.4.2"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "protease site",
+          "val" : "4-methylcytosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m-4C",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N4_methylcytosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m4c",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N4 methylcytosine",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "4-mC",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "N4-methylcytosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T03:36:28Z"
+          "val" : "2012-10-17T12:50:40Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "protease_site"
+      "lbl" : "4_methylcytosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000625",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001918",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A cytosine methylated at the 5 carbon.",
+          "xrefs" : [ "SO:rtapella" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Silencer_(DNA)"
+          "val" : "http://www.insdc.org/files/feature_table.html#7.4.2"
+        }, {
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
         } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "pred" : "hasExactSynonym",
+          "val" : "5 methylcytosine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:silencer",
+          "val" : "5-mC",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m-5C",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "m5c",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-17T12:46:10Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silencer"
+      "lbl" : "5_methylcytosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000620",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001915",
       "meta" : {
         "definition" : {
-          "val" : "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region defined by a cluster of experimentally determined transcription starting sites.",
+          "xrefs" : [ "PMID:19624849", "PMID:21372179", "SO:andrewgibson" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "B-box",
+          "val" : "transcriptional initiation cluster",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TSC",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "transcriptional start site cluster",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "TSS cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Binds TFIIIC."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-10-17T12:09:50Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "B_box"
+      "lbl" : "transcription_start_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001951",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001914",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.",
+          "xrefs" : [ "PMID:14645529" ]
         },
+        "comments" : [ "Requested by Midori - June 2012." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "H3K23me2",
+          "val" : "RTS1 element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3K23 dimethylation site",
+          "val" : "rDNA replication fork barrier",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RTS1 barrier",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "DNA spacer replication fork barrier",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "RFB",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -54716,72 +58662,70 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T11:05:33Z"
+          "val" : "2012-06-11T02:55:02Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H3K23_dimethylation_site"
+      "lbl" : "rDNA_replication_fork_barrier"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001950",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001917",
       "meta" : {
         "definition" : {
-          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region.",
+          "xrefs" : [ "PMID:16645617", "SO:andrewgibson" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : " H4K4me3",
+          "val" : "INSDC_note:CAGE_cluster",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H4K4 trimethylation site",
+          "val" : "CAGE_peak",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_feature",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CAGE peak",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "CAGE cluster",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T11:03:29Z"
+          "val" : "2012-10-17T12:42:03Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "H4K4_trimethylation_site"
+      "lbl" : "CAGE_cluster"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000622",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001916",
       "meta" : {
         "definition" : {
-          "val" : "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites.",
+          "xrefs" : [ "SO:andrewgibson" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "C-box",
+          "val" : "CAGE tag",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "C_box"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001953",
-      "meta" : {
-        "definition" : {
-          "val" : "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends.",
-          "xrefs" : [ "SO:ke" ]
-        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T03:18:11Z"
+          "val" : "2012-10-17T12:36:58Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -54791,32 +58735,52 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "restriction_enzyme_assembly_scar"
+      "lbl" : "CAGE_tag"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000621",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001911",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant where copies of a feature are increased relative to the reference.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNApol III promoter type 3",
+          "val" : "copy number increase",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-13T11:26:32Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNApol_III_promoter_type_3"
+      "lbl" : "copy_number_increase"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001952",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001910",
       "meta" : {
         "definition" : {
-          "val" : "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "promoter flanking region",
+          "val" : "ANNOVAR:frameshift deletion",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:frameshift_truncation",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "frameshift truncation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -54827,246 +58791,268 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-03-06T11:36:25Z"
+          "val" : "2012-04-12T05:10:45Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "promoter_flanking_region"
+      "lbl" : "frameshift_truncation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000660",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001913",
       "meta" : {
+        "definition" : {
+          "val" : "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation.",
+          "xrefs" : [ "Invitrogen:kc" ]
+        },
+        "comments" : [ "Requested by Kevin Clancy - invitrogen -May 2012." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "bacterial RNApol promoter sigma ecf ",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-06-11T02:41:33Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DNA_invertase_target_sequence"
+      "lbl" : "bacterial_RNApol_promoter_sigma_ecf_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001991",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001912",
       "meta" : {
         "definition" : {
-          "val" : "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input.",
-          "xrefs" : [ "GMOD:ea" ]
+          "val" : "A sequence variant where copies of a feature are decreased relative to the reference.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "consensus amplified fragment length polymorphism fragment",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "consensus AFLP fragment",
+          "val" : "copy number decrease",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-09-24T10:43:41Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-04-13T11:27:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Bayer Cropscience September, 2013."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "consensus_AFLP_fragment"
+      "lbl" : "copy_number_decrease"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001990",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001948",
       "meta" : {
         "definition" : {
-          "val" : "A 5' UTR variant where a premature start codon is moved.",
-          "xrefs" : [ "SANGER:am" ]
+          "val" : "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "H3R2 dimethylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H3R2me2",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-31T03:57:47Z"
+          "val" : "2013-03-06T10:59:17Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_UTR_premature_start_codon_location_variant"
+      "lbl" : "H3R2_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000662",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000617",
       "meta" : {
         "definition" : {
-          "val" : "An intron which is spliced by the spliceosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species.",
+          "xrefs" : [ "PMID:12381659" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "spliceosomal intron",
+          "val" : "RNApol III promoter type 1",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "GO:0000398."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "spliceosomal_intron"
+      "lbl" : "RNApol_III_promoter_type_1"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001993",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001947",
       "meta" : {
         "definition" : {
-          "val" : "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after.",
-          "xrefs" : [ "SANGER:am" ]
+          "val" : "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "extended cis splice site",
+          "val" : " H3R2me1",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H3R2 monomethylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added by Andy Menzies (Sanger)."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T10:57:13Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-04T06:20:00Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "extended_cis_splice_site"
+      "lbl" : "H3R2_monomethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001992",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000616",
       "meta" : {
         "definition" : {
-          "val" : "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change.",
+          "val" : "The base where transcription ends.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "nonsynonymous variant",
+          "val" : "transcription end site",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non_synonymous_coding",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-10-16T11:47:51Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nonsynonymous_variant"
+      "lbl" : "transcription_end_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000661",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000619",
       "meta" : {
+        "definition" : {
+          "val" : "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Binds TFIIIC." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/A-box"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "A-box",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intron_attribute"
+      "lbl" : "A_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001508",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000618",
       "meta" : {
+        "definition" : {
+          "val" : "This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box.",
+          "xrefs" : [ "PMID:12381659" ]
+        },
         "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "tRNA promoter",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "alteration attribute",
+          "val" : "RNApol III promoter type 2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:53:23Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alteration_attribute"
+      "lbl" : "RNApol_III_promoter_type_2"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001507",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001949",
       "meta" : {
         "definition" : {
-          "val" : "A collection of one or more sequences of an individual.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "variant collection",
+          "pred" : "hasExactSynonym",
+          "val" : "H4R3 dimethylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H4R3me2",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-03T02:13:28Z"
+          "val" : "2013-03-06T11:01:27Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "variant_collection"
+      "lbl" : "H4R3_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001509",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000613",
       "meta" : {
+        "definition" : {
+          "val" : "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "chromosomal variation attribute",
+          "val" : "bacterial RNApol promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:54:30Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomal_variation_attribute"
+      "lbl" : "bacterial_RNApol_promoter"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001504",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001944",
       "meta" : {
         "definition" : {
-          "val" : "A chromosome variation derived from an event during meiosis.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "assortment derived variation",
+          "pred" : "hasExactSynonym",
+          "val" : "H2AK9 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2AK9ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55074,33 +59060,28 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-02T05:03:18Z"
+          "val" : "2013-03-06T10:48:11Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "assortment_derived_variation"
+      "lbl" : "H2AK9_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000657",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000612",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence containing one or more repeat units.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing.",
+          "xrefs" : [ "http://nar.oupjournals.org/cgi/content/full/25/4/888" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Polypyrimidine_tract"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "repeat region",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:other",
+          "val" : "polypyrimidine tract",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55109,101 +59090,124 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "repeat_region"
+      "lbl" : "polypyrimidine_tract"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001988",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001943",
       "meta" : {
         "definition" : {
-          "val" : "A 5' UTR variant where a premature start codon is gained.",
-          "xrefs" : [ "Sanger:am" ]
+          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:START_GAINED",
+          "val" : "H3K4ac",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:5_prime_UTR_premature_start_codon_gain_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5 prime UTR premature start codon gain variant",
+          "val" : "H3K4 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T10:46:32Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-31T03:53:06Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_premature_start_codon_gain_variant"
+      "lbl" : "H3K4_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001987",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001946",
       "meta" : {
+        "definition" : {
+          "val" : "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "downstream transcript variant",
+          "val" : "H2BK15ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2BK15 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Graham Ritchie, EBI/Sanger."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-31T03:47:51Z"
+          "val" : "2013-03-06T10:53:23Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "downstream_transcript_variant"
+      "lbl" : "H2BK15_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001503",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000615",
       "meta" : {
         "definition" : {
-          "val" : "A transcript for which no open reading frame has been identified and for which no other function has been determined.",
-          "xrefs" : [ "MGI:hdeen" ]
+          "val" : "A terminator signal for RNA polymerase III transcription.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "processed transcript",
+          "val" : "terminator of type 2 RNApol III promoter",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Ensembl and Vega also use this term name. Requested by Howard Deen of MGI."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-12-21T05:37:14Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "terminator_of_type_2_RNApol_III_promoter"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001945",
+      "meta" : {
+        "definition" : {
+          "val" : "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "H3K56ac",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H3K56 acetylation site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T10:51:14Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "processed_transcript"
+      "lbl" : "H3K56_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000656",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000614",
       "meta" : {
+        "definition" : {
+          "val" : "A terminator signal for bacterial transcription.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Moved to transcriptional_cis_regulatory_region (SO:0001055) from gene_group_regulatory_region (SO:0000752) on 11 Feb 2021 when SO:0000752 was merged into SO:0001055. See GitHub Issue #529." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "stRNA encoding",
+          "val" : "bacterial terminator",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55212,73 +59216,87 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stRNA_encoding"
+      "lbl" : "bacterial_terminator"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000659",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001940",
       "meta" : {
+        "definition" : {
+          "val" : "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj", "http://dx.doi.org/10.4161/epi.6.5.15623" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tmRNA encoding",
+          "val" : "H2BK120ac",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2BK120 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T10:28:38Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tmRNA_encoding"
+      "lbl" : "H2BK120_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001506",
+      "id" : "http://purl.obolibrary.org/obo/so#dbsnp",
+      "lbl" : "dbsnp variant terms"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001942",
       "meta" : {
         "definition" : {
-          "val" : "A collection of sequences (often chromosomes) of an individual.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "variant genome",
+          "pred" : "hasExactSynonym",
+          "val" : "H2BK20 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2BK20ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-03T02:11:25Z"
+          "val" : "2013-03-06T10:44:31Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "variant_genome"
+      "lbl" : "H2BK20_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000658",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000611",
       "meta" : {
         "definition" : {
-          "val" : "A repeat that is located at dispersed sites in the genome.",
+          "val" : "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat.",
           "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Interspersed_repeat"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:dispersed",
+          "val" : "branch_point",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "interspersed repeat",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "val" : "branch site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "dispersed repeat",
+          "val" : "branch point",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55287,17 +59305,26 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "dispersed_repeat"
+      "lbl" : "branch_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001989",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001941",
       "meta" : {
         "definition" : {
-          "val" : "A 5' UTR variant where a premature start codon is lost.",
-          "xrefs" : [ "SANGER:am" ]
+          "val" : "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "H4K91 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H4K91ac",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-31T03:56:48Z"
+          "val" : "2013-03-06T10:41:04Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -55307,147 +59334,138 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_premature_start_codon_loss_variant"
+      "lbl" : "H4K91_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001505",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000610",
       "meta" : {
         "definition" : {
-          "val" : "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.",
+          "val" : "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "reference genome",
+          "pred" : "hasExactSynonym",
+          "val" : "polyA sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-03T02:10:03Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reference_genome"
+      "lbl" : "polyA_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000653",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000609",
       "meta" : {
         "definition" : {
-          "val" : "A component of the large ribosomal subunit.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602).",
+          "xrefs" : [ "http://www.rna.ucla.edu/" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/28S_ribosomal_RNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "28S ribosomal RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "rRNA 28S",
+          "val" : "oligo U tail",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "oligo_U_tail"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001937",
+      "meta" : {
+        "definition" : {
+          "val" : "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "28S LSU rRNA",
+          "val" : "H2BK12ac",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "28S rRNA",
+          "val" : "H2BK12 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T10:19:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_28S"
+      "lbl" : "H2BK12_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001984",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000606",
       "meta" : {
         "definition" : {
-          "val" : "A gene cassette array that corresponds to a silenced version of a mating type region.",
-          "xrefs" : [ "PomBase:mah" ]
+          "val" : "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602).",
+          "xrefs" : [ "http://dna.kdna.ucla.edu/rna/index.aspx" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "silent mating-type cassette",
+          "pred" : "hasExactSynonym",
+          "val" : "editing domain",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-31T02:40:38Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "silent_mating_type_cassette_array"
+      "lbl" : "editing_domain"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001500",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001936",
       "meta" : {
         "definition" : {
-          "val" : "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.",
-          "xrefs" : [ "JAX:hdene" ]
+          "val" : "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "heritable phenotypic marker",
+          "val" : "H3K36ac",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "phenotypic marker",
+          "val" : "H3K36 acetylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-12-07T01:50:55Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2013-03-06T10:16:55Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "heritable_phenotypic_marker"
+      "lbl" : "H3K36_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000652",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000605",
       "meta" : {
         "definition" : {
-          "val" : "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription.",
-          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001" ]
+          "val" : "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome.",
+          "xrefs" : [ "SO:cjm" ]
         },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/5S_ribosomal_RNA"
+          "val" : "http://en.wikipedia.org/wiki/Intergenic_region"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA 5S",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5S rRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5S LSU rRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "5S ribosomal RNA",
+          "val" : "intergenic region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55456,81 +59474,69 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_5S"
+      "lbl" : "intergenic_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001983",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000608",
       "meta" : {
         "definition" : {
-          "val" : "A 5' UTR variant where a premature start codon is introduced, moved or lost.",
-          "xrefs" : [ "SANGER:am" ]
+          "val" : "snoRNA that is associated with guiding polyuridylation. It contains two short conserved sequence motifs: H box (ANANNA) and ACA (ACA).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5' UTR premature start codon variant",
+          "val" : "H ACA box snoRNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T04:36:25Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "5_prime_UTR_premature_start_codon_variant"
+      "lbl" : "H_ACA_box_snoRNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000655",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001939",
       "meta" : {
         "definition" : {
-          "val" : "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/NcRNA"
-        }, {
-          "val" : "http://www.gencodegenes.org/gencode_biotypes.html"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_qualifier:other",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "noncoding RNA",
+          "val" : "H4K12 acetylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "known_ncrna",
+          "val" : "H4K12ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T10:26:15Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ncRNA"
+      "lbl" : "H4K12_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001986",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001938",
       "meta" : {
         "definition" : {
-          "val" : "A feature variant, where the alteration occurs upstream of the transcript TSS.",
-          "xrefs" : [ "EBI:gr" ]
+          "val" : "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "upstream transcript variant",
+          "val" : "H2AK5 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H2AK5ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55538,170 +59544,139 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-31T03:46:14Z"
+          "val" : "2013-03-06T10:20:57Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Graham Ritchie, EBI/Sanger."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "upstream_transcript_variant"
+      "lbl" : "H2AK5_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001502",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000607",
       "meta" : {
         "definition" : {
-          "val" : "An experimental feature with high sequence identity to another sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "The region of an edited transcript that will not be edited.",
+          "xrefs" : [ "http://dna.kdna.ucla.edu/rna/index.aspx" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "high identity region",
+          "val" : "unedited region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-12-11T11:06:05Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by tracker ID: 2902685."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "high_identity_region"
+      "lbl" : "unedited_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001985",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001933",
       "meta" : {
         "definition" : {
-          "val" : "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication.",
-          "xrefs" : [ "ISBN:0805350152" ]
+          "val" : "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Okazaki fragment",
+          "val" : "restriction enzyme three prime single strand overhang",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-31T02:57:55Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Midori Harris, 2013."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T09:52:14Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "Okazaki_fragment"
+      "lbl" : "restriction_enzyme_three_prime_single_strand_overhang"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001501",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000602",
       "meta" : {
         "definition" : {
-          "val" : "A collection of peptide sequences.",
-          "xrefs" : [ "BBOP:nlw" ]
+          "val" : "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA.",
+          "xrefs" : [ "http://www.rna.ucla.edu/index.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Guide_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "peptide set",
+          "val" : "guide RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "peptide collection",
+          "val" : "gRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:guide_RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-12-11T10:58:58Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Term requested via tracker ID: 2910829."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "peptide_collection"
+      "lbl" : "guide_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000654",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000601",
       "meta" : {
-        "definition" : {
-          "val" : "A mitochondrial gene located in a maxicircle.",
-          "xrefs" : [ "SO:xp" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "maxicircle gene",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "maxi-circle gene",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "maxicircle_gene"
+      "lbl" : "edited_by_G_addition"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001980",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001932",
       "meta" : {
         "definition" : {
-          "val" : "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a.",
-          "xrefs" : [ "PMID:19249238", "PMID:8571452", "SO:ml" ]
+          "val" : "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "GBF binding sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "G-box",
+          "val" : "restriction enzyme five prime single strand overhang",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A plant specific region."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T09:50:44Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T04:00:50Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "G_box"
+      "lbl" : "restriction_enzyme_five_prime_single_strand_overhang"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001982",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001935",
       "meta" : {
         "definition" : {
-          "val" : "A plant regulatory promoter motif,  composed of a highly conserved hexamer GATAAG (I-box core).",
-          "xrefs" : [ "PMID:2347304", "PMID:2902624", "SO:ml" ]
+          "val" : "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "I-box promoter motif",
+          "val" : "H3K20 trimethylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55712,30 +59687,21 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T04:17:55Z"
+          "val" : "2013-03-06T10:13:48Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "I-box"
+      "lbl" : "H3K20_trimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000651",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000604",
       "meta" : {
         "definition" : {
-          "val" : "Ribosomal RNA transcript that structures the large subunit of the ribosome.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Edited mRNA sequence mediated by a single guide RNA (SO:0000602).",
+          "xrefs" : [ "http://dna.kdna.ucla.edu/rna/index.aspx" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "LSU RNA",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "LSU rRNA",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "large subunit rRNA",
+          "val" : "editing block",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55744,169 +59710,133 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "large_subunit_rRNA"
+      "lbl" : "editing_block"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001981",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000603",
       "meta" : {
         "definition" : {
-          "val" : "An orientation dependent  regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants.",
-          "xrefs" : [ "PMID:17381552", "PMID:2902624", "SO:ml" ]
+          "val" : "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny.",
+          "xrefs" : [ "http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml" ]
         },
+        "comments" : [ "GO:0000373." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Group_II_intron"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "L-box promoter element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "L-box",
+          "val" : "group II intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T04:12:19Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "L_box"
+      "lbl" : "group_II_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000650",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001934",
       "meta" : {
         "definition" : {
-          "val" : "Ribosomal RNA transcript that structures the small subunit of the ribosome.",
+          "val" : "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SSU RNA",
-          "xrefs" : [ "RSC:cb" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small subunit rRNA",
+          "val" : "monomeric repeat",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "SSU rRNA",
-          "xrefs" : [ "RSC:cb" ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T09:59:15Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "small_subunit_rRNA"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/so#RNAMOD",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasScope",
-          "val" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
-        } ]
-      },
-      "type" : "PROPERTY",
-      "lbl" : "RNA modification"
+      "lbl" : "monomeric_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000646",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001931",
       "meta" : {
         "definition" : {
-          "val" : "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules.",
-          "xrefs" : [ "PMID:12592000" ]
+          "val" : "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input.",
+          "xrefs" : [ "GMOD:ea" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/SiRNA"
-        } ],
+        "comments" : [ "Requested by Bayer Cropscience November, 2012." ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:siRNA",
+          "val" : "consensus genomic DNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "small interfering RNA",
+          "val" : "consensus gDNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2012-11-28T12:53:14Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "siRNA"
+      "lbl" : "consensus_gDNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001977",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000600",
       "meta" : {
-        "definition" : {
-          "val" : "A region of a transcript encoding the cleavage site for a ribonuclease enzyme.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "ribonuclease site",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T11:41:06Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "ribonuclease_site"
+      "lbl" : "edited_by_A_to_I_substitution"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001976",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001930",
       "meta" : {
         "definition" : {
-          "val" : "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequencer read of a chloroplast DNA sample.",
+          "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience, October, 2012." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime sticky end restriction enzyme cleavage site",
+          "val" : "chloroplast DNA read",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T11:37:19Z"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by  Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2012-11-14T04:43:45Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_sticky_end_restriction_enzyme_cleavage_site"
+      "lbl" : "chloroplast_DNA_read"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000645",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000640",
       "meta" : {
         "definition" : {
-          "val" : "The reverse complement of the primary transcript.",
+          "val" : "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "antisense primary transcript",
+          "val" : "external transcribed spacer region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55915,17 +59845,22 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "antisense_primary_transcript"
+      "lbl" : "external_transcribed_spacer_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001979",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001971",
       "meta" : {
         "definition" : {
-          "val" : "A motif that affects the stability of RNA.",
-          "xrefs" : [ "PMID:22495308", "SO:ke" ]
+          "val" : "A binding site to which a polypeptide will bind with a zinc finger motif, which is characterized by requiring one or more Zinc 2+ ions for stabilized folding.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "RNA stability element",
+          "val" : "zinc_fing",
+          "xrefs" : [ "unirot:features" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "zinc finger binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -55936,112 +59871,109 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T03:33:53Z"
+          "val" : "2013-07-29T04:41:53Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "RNA_stability_element"
+      "lbl" : "zinc_finger_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000647",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001970",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a micro RNA.",
+          "val" : "A transcript variant occurring within an intron of a non coding transcript.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "micro RNA primary transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "miRNA primary transcript",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "small temporal RNA primary transcript",
-          "xrefs" : [ ]
+          "pred" : "hasNarrowSynonym",
+          "val" : "ANNOVAR:ncRNA_intronic",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "stRNA primary transcript",
+          "val" : "non coding transcript intron variant",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "stRNA_primary_transcript",
-          "xrefs" : [ ]
+          "pred" : "hasNarrowSynonym",
+          "val" : "Jannovar:non_coding_transcript_intron_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0000648"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-05-23T10:55:03Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "miRNA_primary_transcript"
+      "lbl" : "non_coding_transcript_intron_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001978",
+      "id" : "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty",
+      "type" : "PROPERTY",
+      "lbl" : "synonym_type_property"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000639",
       "meta" : {
         "definition" : {
-          "val" : "A region of  sequence where developer information is encoded.",
+          "val" : "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DNA signature",
+          "val" : "internal transcribed spacer region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T11:49:22Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Jackie Quinn for use in synthetic biology."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "signature"
+      "lbl" : "internal_transcribed_spacer_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001973",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001969",
       "meta" : {
         "definition" : {
-          "val" : "A histone 3 modification where the modification is the acetylation of the residue.",
-          "xrefs" : [ "EBI:nj", "ISBN:0815341059", "SO:ke" ]
+          "val" : "A transcript variant occurring within an intron of a coding transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histone 3 acetylation site",
+          "val" : "coding sequence intron variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H3ac",
-          "xrefs" : [ ]
+          "val" : "Jannovar:coding_transcript_intron_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T10:46:42Z"
+          "val" : "2013-05-23T10:54:17Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histone_3_acetylation_site"
+      "lbl" : "coding_transcript_intron_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000642",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000638",
       "meta" : {
+        "definition" : {
+          "val" : "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA.",
+          "xrefs" : [ "http://oregonstate.edu/instruction/bb492/general/glossary.html" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SRP RNA encoding",
+          "val" : "transcribed spacer region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56050,101 +59982,79 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SRP_RNA_encoding"
+      "lbl" : "transcribed_spacer_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001972",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001966",
       "meta" : {
         "definition" : {
-          "val" : "A histone 4 modification where the modification is the acetylation of the residue.",
-          "xrefs" : [ "EBI:nj", "ISBN:0815341059", "SO:ke" ]
+          "val" : "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histone 4 acetylation site",
+          "val" : "5-caC",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "H4ac",
+          "val" : "5-carboxycytosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T10:43:04Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-05-20T01:30:01Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histone_4_acetylation_site"
+      "lbl" : "5_carboxylcytosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000641",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "tetranucleotide repeat microsatellite feature",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "tetranucleotide_repeat_microsatellite_feature"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001975",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000635",
       "meta" : {
         "definition" : {
-          "val" : "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs.",
+          "val" : "A primary transcript that donates the spliced leader to other mRNA.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "five prime sticky end restriction enzyme cleavage site",
+          "val" : "mini exon donor RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "mini-exon donor RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by  Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T11:32:16Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_sticky_end_restriction_enzyme_cleavage_site"
+      "lbl" : "mini_exon_donor_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000644",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000634",
       "meta" : {
         "definition" : {
-          "val" : "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An mRNA that encodes multiple proteins from at least two non-overlapping regions.",
+          "xrefs" : [ "SO:rd" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Antisense_RNA"
+          "val" : "http://en.wikipedia.org/wiki/Polycistronic_mRNA"
         } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:ncRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "antisense RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "polycistronic processed transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:antisense_RNA",
+          "val" : "polycistronic mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56153,58 +60063,53 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "antisense_RNA"
+      "lbl" : "polycistronic_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001974",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001965",
       "meta" : {
         "definition" : {
-          "val" : "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor.",
-          "xrefs" : [ "EBI:nj" ]
+          "val" : "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "CCCTF binding site",
+          "val" : "8-oxoguanine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "CTCF binding site",
+          "val" : "8-oxoG",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-05-20T01:27:51Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2013-07-30T10:59:11Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "CTCF_binding_site"
+      "lbl" : "8_oxoguanine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000643",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000637",
       "meta" : {
         "definition" : {
-          "val" : "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.",
-          "xrefs" : [ "http://www.informatics.jax.org/silver/glossary.shtml" ]
+          "val" : "A plasmid that is engineered.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Minisatellite"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VNTR",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:minisatellite",
+          "val" : "engineered plasmid",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:repeat_region",
+          "pred" : "hasRelatedSynonym",
+          "val" : "engineered plasmid gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56213,106 +60118,83 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minisatellite"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000682",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "splicing_feature"
+      "lbl" : "engineered_plasmid"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000681",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001968",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons.",
+          "val" : "A transcript variant of a protein coding gene.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "aberrant processed transcript",
+          "val" : "coding transcript variant",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "aberrant_processed_transcript"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000684",
-      "meta" : {
-        "definition" : {
-          "val" : "A region of nucleotide sequence targeted by a nuclease enzyme.",
-          "xrefs" : [ "SO:ma" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "nuclease sensitive site",
-          "xrefs" : [ ]
+          "val" : "Jannovar:coding_transcript_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-05-22T04:34:49Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclease_sensitive_site"
+      "lbl" : "coding_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001531",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001967",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide region that targets a polypeptide to he cytoplasm.",
+          "val" : "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Nuclear_export_signal"
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "NES",
+          "val" : "8-oxoadenine",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "nuclear export signal",
+          "val" : "8-oxoA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T02:25:25Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2013-05-20T01:31:05Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclear_export_signal"
+      "lbl" : "8_oxoadenine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000200",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000636",
       "meta" : {
         "definition" : {
-          "val" : "The 5' most coding exon.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Snall nuclear RNAs that are incorporated into the pre-mRNAs to replace the 5' end in some eukaryotes.",
+          "xrefs" : [ "PMID:24130571" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "5' coding exon",
+          "pred" : "hasRelatedSynonym",
+          "val" : "mini-exon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "five prime coding exon",
+          "val" : "spliced leader RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56321,17 +60203,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_coding_exon"
+      "lbl" : "spliced_leader_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000683",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000631",
       "meta" : {
         "definition" : {
-          "val" : "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract" ]
+          "val" : "A primary transcript encoding for more than one gene product.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "exonic splice enhancer",
+          "val" : "polycistronic primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56340,102 +60222,95 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exonic_splice_enhancer"
+      "lbl" : "polycistronic_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001530",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001962",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide region that targets a polypeptide to the lysosome.",
+          "val" : "A modified adenine DNA base feature.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "lysosomal localization signal",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T02:24:10Z"
+          "val" : "2013-05-20T01:22:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lysosomal_localization_signal"
+      "lbl" : "modified_adenine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000680",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001961",
       "meta" : {
         "definition" : {
-          "val" : "A start codon that is not the usual AUG sequence.",
+          "val" : "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non ATG start codon",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non-canonical start codon",
+          "val" : "5-fC",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non canonical start codon",
+          "val" : "5-formylcytosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-05-17T05:06:13Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_canonical_start_codon"
+      "lbl" : "5_formylcytosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001529",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000630",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide region that targets a polypeptide to the endosome.",
+          "val" : "A start codon upstream of the ORF.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "endosomal localization signal",
+          "val" : "upstream AUG codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T02:20:58Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "endosomal_localization_signal"
+      "lbl" : "upstream_AUG_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000679",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000633",
       "meta" : {
         "definition" : {
-          "val" : "A 5' splice site which does not have the sequence \"GT\".",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap.",
+          "xrefs" : [ "SO:rd" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Monocistronic_mRNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non canonical five prime splice site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non-canonical five prime splice site",
+          "val" : "monocistronic processed transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non canonical 5' splice site",
+          "val" : "monocistronic mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56444,75 +60319,57 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_canonical_five_prime_splice_site"
+      "lbl" : "monocistronic_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001526",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001964",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.",
+          "val" : "A modified guanine DNA base feature.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "base call error correction",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-09T02:18:07Z"
+          "val" : "2013-05-20T01:25:31Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "base_call_error_correction"
+      "lbl" : "modified_guanine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001525",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001963",
       "meta" : {
         "definition" : {
-          "val" : "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.",
+          "val" : "A modified cytosine DNA base feature.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "assembly error correction",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-09T02:16:31Z"
+          "val" : "2013-05-20T01:23:47Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "assembly_error_correction"
+      "lbl" : "modified_cytosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000678",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000632",
       "meta" : {
         "definition" : {
-          "val" : "A 3' splice site that does not have the sequence \"AG\".",
+          "val" : "A primary transcript encoding for one gene product.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non-canonical three prime splice site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "non canonical 3' splice site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "non canonical three prime splice site",
+          "val" : "monocistronic primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56521,55 +60378,58 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_canonical_three_prime_splice_site"
+      "lbl" : "monocistronic_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001528",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001960",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide region that targets a polypeptide to the nucleus.",
+          "val" : "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Nuclear_localization_signal"
+          "val" : "http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "NLS",
+          "val" : "5-hmC",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5-hydroxymethylcytosine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T02:16:38Z"
+          "val" : "2013-05-17T05:05:31Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclear_localization_signal"
+      "lbl" : "5_hydroxymethylcytosine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001527",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001959",
       "meta" : {
         "definition" : {
-          "val" : "A region of peptide sequence used to target the polypeptide molecule to a specific organelle.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator.",
+          "xrefs" : [ "PMID:20801935", "SO:myl" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "localization signal",
+          "pred" : "hasExactSynonym",
+          "val" : "polypyrimidine initiator",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "peptide localization signal",
+          "val" : "TCT element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T02:15:05Z"
+          "val" : "2013-05-17T04:38:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -56579,134 +60439,95 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "peptide_localization_signal"
+      "lbl" : "TCT_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000675",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000628",
       "meta" : {
         "definition" : {
-          "val" : "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Regions of the chromosome that are important for structural elements.",
+          "xrefs" : [ ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "canonical splice site",
+          "val" : "chromosomal structural element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0000676"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0000677"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "canonical_splice_site"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001522",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:59:51Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "insertional"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001521",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:59:34Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reciprocal"
+      "lbl" : "chromosomal_structural_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000674",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000627",
       "meta" : {
         "definition" : {
-          "val" : "A splice site where the donor and acceptor sites differ from the canonical form.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region.",
+          "xrefs" : [ "NCBI:cf", "PMID:12154228", "SO:regcreative" ]
         },
+        "comments" : [ "moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Insulator_(genetics)"
+        } ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "non canonical splice site",
+          "val" : "INSDC_qualifier:insulator",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non-canonical splice site",
+          "val" : "insulator element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0000678"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
-          "val" : "SO:0000679"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_canonical_splice_site"
+      "lbl" : "insulator"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001524",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001958",
       "meta" : {
+        "definition" : {
+          "val" : "A kind of intron whereby the excision is driven by lariat formation.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Requested by PomBase 3604508." ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "chromosomally aberrant genome",
+          "pred" : "hasExactSynonym",
+          "val" : "lariat intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-05T02:21:00Z"
+          "val" : "2013-03-07T10:58:40Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosomally_aberrant_genome"
+      "lbl" : "lariat_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000677",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000629",
       "meta" : {
         "definition" : {
-          "val" : "The canonical 5' splice site has the sequence \"GT\".",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An open reading frame found within the 5' UTR that can be translated and stall the translation of the downstream open reading frame.",
+          "xrefs" : [ "PMID:12890013" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "canonical 5' splice site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "canonical five prime splice site",
+          "val" : "five prime open reading frame",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56715,21 +60536,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "canonical_five_prime_splice_site"
+      "lbl" : "five_prime_open_reading_frame"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000676",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000624",
       "meta" : {
         "definition" : {
-          "val" : "The canonical 3' splice site has the sequence \"AG\".",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Telomere"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "canonical three prime splice site",
+          "val" : "INSDC_feature:telomere",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "canonical 3' splice site",
+          "val" : "telomeric sequence",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "telomeric DNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56738,38 +60567,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "canonical_three_prime_splice_site"
+      "lbl" : "telomere"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001523",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001955",
       "meta" : {
+        "definition" : {
+          "val" : "A polypeptide region that proves structure in a protein that affects the stability of the protein.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "duplication attribute",
+          "val" : "protein stability element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T03:32:47Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-05T01:56:33Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "duplication_attribute"
+      "lbl" : "protein_stability_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000671",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000623",
       "meta" : {
         "definition" : {
-          "val" : "A sequence eliminated from the genome of ciliates during nuclear differentiation.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A region that can be transcribed into a small nuclear RNA (snRNA).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "internal eliminated sequence",
+          "val" : "snRNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56778,80 +60611,96 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "internal_eliminated_sequence"
+      "lbl" : "snRNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000670",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001954",
       "meta" : {
         "definition" : {
-          "val" : "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A region related to restriction enzyme function.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Not a great term for annotation, but used to classify the various regions related to restriction enzymes." ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "chromosome breakage sequence",
+          "pred" : "hasRelatedSynonym",
+          "val" : "restriction enzyme region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T03:23:34Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "chromosome_breakage_sequence"
+      "lbl" : "restriction_enzyme_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000673",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001957",
       "meta" : {
         "definition" : {
-          "val" : "An RNA synthesized on a DNA or RNA template by an RNA polymerase.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "RNA secondary structure that affects the stability of an RNA molecule.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/RNA"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:misc_RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "rna stability element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T03:38:35Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "transcript"
+      "lbl" : "RNA_stability_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001520",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000626",
       "meta" : {
+        "definition" : {
+          "val" : "Regions of the chromosome that are important for regulating binding of chromosomes to the nuclear matrix.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translocation attribute",
+          "val" : "chromosomal regulatory element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:58:47Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translocaton_attribute"
+      "lbl" : "chromosomal_regulatory_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000672",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000625",
       "meta" : {
         "definition" : {
-          "val" : "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Silencer_(DNA)"
+        } ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "macronucleus destined segment",
+          "val" : "INSDC_qualifier:silencer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -56860,238 +60709,184 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "macronucleus_destined_segment"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001519",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:58:35Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "paracentric"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001518",
-      "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:58:24Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "pericentric"
+      "lbl" : "silencer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001999",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001956",
       "meta" : {
         "definition" : {
-          "val" : "DNA motif that is a component of a mating type region.",
+          "val" : "A polypeptide_region that codes for a protease cleavage site.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "mating type region motif",
+          "val" : "protease site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T03:36:28Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:30:17Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mating_type_region_motif"
+      "lbl" : "protease_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000668",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001951",
       "meta" : {
         "definition" : {
-          "val" : "A match against an EST sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "EST match",
+          "val" : "H3K23me2",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H3K23 dimethylation site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "EST_match"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001515",
-      "meta" : {
-        "definition" : {
-          "val" : "A quality of an insertion where the insert is in a cytologically inverted orientation.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:57:40Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-03-06T11:05:33Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inverted"
+      "lbl" : "H3K23_dimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000667",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000620",
       "meta" : {
         "definition" : {
-          "val" : "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.",
+          "val" : "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#DBVAR" ],
-        "xrefs" : [ {
-          "val" : "loinc:LA6687-3"
-        } ],
+        "comments" : [ "Binds TFIIIC." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "insertion",
-          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nucleotide_insertion",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nucleotide insertion",
+          "val" : "B-box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:1000034"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insertion"
+      "lbl" : "B_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001998",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001950",
       "meta" : {
         "definition" : {
-          "val" : "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method.",
-          "xrefs" : [ "PMID:23934893" ]
+          "val" : "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated.",
+          "xrefs" : [ "EBI:nj" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "gRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "guide RNA",
+          "pred" : "hasExactSynonym",
+          "val" : "H4K4 trimethylation site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "small guide RNA",
+          "val" : " H4K4me3",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:25:08Z"
+          "val" : "2013-03-06T11:03:29Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sgRNA"
+      "lbl" : "H4K4_trimethylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001514",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001953",
       "meta" : {
         "definition" : {
-          "val" : "A quality of an insertion where the insert is not in a cytologically inverted orientation.",
+          "val" : "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends.",
           "xrefs" : [ "SO:ke" ]
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:56:49Z"
+          "val" : "2013-03-06T03:18:11Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "direct"
+      "lbl" : "restriction_enzyme_assembly_scar"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001517",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000622",
       "meta" : {
+        "definition" : {
+          "val" : "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inversion attribute",
+          "val" : "C-box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:58:10Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inversion_attribute"
+      "lbl" : "C_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001516",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001952",
       "meta" : {
         "definition" : {
-          "val" : "The quality of a duplication where the new region exists independently of the original.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites.",
+          "xrefs" : [ "EBI:nj" ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "promoter flanking region",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:57:51Z"
+          "val" : "2013-03-06T11:36:25Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "free"
+      "lbl" : "promoter_flanking_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000669",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000621",
       "meta" : {
+        "definition" : {
+          "val" : "This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream. ",
+          "xrefs" : [ "PMID:12381659" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence rearrangement feature",
+          "val" : "RNApol III promoter type 3",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57100,57 +60895,83 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_rearrangement_feature"
+      "lbl" : "RNApol_III_promoter_type_3"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001995",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001991",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant occurring in the intron, within 10 bases of exon.",
-          "xrefs" : [ "sanger:am" ]
+          "val" : "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input.",
+          "xrefs" : [ "GMOD:ea" ]
         },
+        "comments" : [ "Requested by Bayer Cropscience September, 2013." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "extended intronic splice region variant",
+          "val" : "consensus AFLP fragment",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "consensus amplified fragment length polymorphism fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-04T06:37:27Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Added by Andy Menzies (Sanger)."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-09-24T10:43:41Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "extended_intronic_splice_region_variant"
+      "lbl" : "consensus_AFLP_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001511",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000660",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "DNA_invertase_target_sequence"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001990",
       "meta" : {
+        "definition" : {
+          "val" : "A 5' UTR variant where a premature start codon is moved.",
+          "xrefs" : [ "SANGER:am" ]
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:55:43Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2013-07-31T03:57:47Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "interchromosomal"
+      "lbl" : "five_prime_UTR_premature_start_codon_location_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000664",
+      "id" : "http://purl.obolibrary.org/obo/so#AGR",
+      "lbl" : "Alliance of Genome Resources"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000662",
       "meta" : {
+        "definition" : {
+          "val" : "An intron which is spliced by the spliceosome.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "GO:0000398." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "introgressed chromosome region",
+          "val" : "spliceosomal intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57159,50 +60980,49 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "introgressed_chromosome_region"
+      "lbl" : "spliceosomal_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001994",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001993",
       "meta" : {
         "definition" : {
-          "val" : "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron.",
+          "val" : "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after.",
           "xrefs" : [ "SANGER:am" ]
         },
+        "comments" : [ "Added by Andy Menzies (Sanger)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "intron base 5",
+          "val" : "extended cis splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-04T06:26:02Z"
+          "val" : "2014-01-04T06:20:00Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intron_base_5"
+      "lbl" : "extended_cis_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000663",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001992",
       "meta" : {
+        "definition" : {
+          "val" : "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tRNA encoding",
+          "val" : "non_synonymous_coding",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "nonsynonymous variant",
           "xrefs" : [ ]
         } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "tRNA_encoding"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001510",
-      "meta" : {
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -57211,100 +61031,101 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:55:25Z"
+          "val" : "2013-10-16T11:47:51Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intrachromosomal"
+      "lbl" : "nonsynonymous_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001513",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000661",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:56:37Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "tandem"
+      "lbl" : "intron_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001997",
+      "id" : "http://purl.obolibrary.org/obo/BS_00232",
       "meta" : {
-        "definition" : {
-          "val" : "A heterochromatic region of the chromosome,  adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed.",
-          "xrefs" : [ "POMBE:al" ]
-        },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-05T07:02:01Z"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001143"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "subtelomere"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000666",
+      "id" : "http://purl.obolibrary.org/obo/BS_00231",
       "meta" : {
-        "definition" : {
-          "val" : "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mobile intron",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001141"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00230",
+      "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001127"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "mobile_intron"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000665",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001508",
       "meta" : {
         "definition" : {
-          "val" : "A transcript that is monocistronic.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An attribute of alteration of one or more chromosomes.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "monocistronic transcript",
+          "val" : "alteration attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:53:23Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "monocistronic_transcript"
+      "lbl" : "alteration_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001512",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001507",
       "meta" : {
         "definition" : {
-          "val" : "A quality of a chromosomal insertion,.",
+          "val" : "A collection of one or more sequences of an individual.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "insertion attribute",
+          "pred" : "hasRelatedSynonym",
+          "val" : "variant collection",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-04T02:55:56Z"
+          "val" : "2010-03-03T02:13:28Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -57314,22 +61135,48 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "insertion_attribute"
+      "lbl" : "variant_collection"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001996",
+      "id" : "http://purl.obolibrary.org/obo/BS_00235",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001144"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00234",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001142"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001509",
       "meta" : {
         "definition" : {
-          "val" : "Region of intronic sequence within 10 bases of an exon.",
-          "xrefs" : [ "SANGER:am" ]
+          "val" : "An attribute of a change in the structure or number of a chromosomes.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "extended intronic splice region ",
+          "val" : "chromosomal variation attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2014-01-04T06:41:23Z"
+          "val" : "2010-03-04T02:54:30Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
@@ -57339,17 +61186,39 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "extended_intronic_splice_region"
+      "lbl" : "chromosomal_variation_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000220",
+      "id" : "http://purl.obolibrary.org/obo/BS_00233",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001145"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000657",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding isoleucyl tRNA (SO:0000263).",
+          "val" : "A region of sequence containing one or more repeat units.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "isoleucine tRNA primary transcript",
+          "val" : "INSDC_qualifier:other",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "repeat region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57358,67 +61227,81 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "isoleucine_tRNA_primary_transcript"
+      "lbl" : "repeat_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001551",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001988",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that increases the rate of transcription with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A 5' UTR variant where a premature start codon is gained.",
+          "xrefs" : [ "Sanger:am" ]
         },
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "increased transcription rate variant",
+          "val" : "Jannovar:5_prime_UTR_premature_start_codon_gain_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5 prime UTR premature start codon gain variant",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:START_GAINED",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:52:17Z"
+          "val" : "2013-07-31T03:53:06Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "increased_transcription_rate_variant"
+      "lbl" : "5_prime_UTR_premature_start_codon_gain_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001550",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001504",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the rate of transcription with respect to a reference sequence.",
+          "val" : "A chromosome variation derived from an event during meiosis.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "rate of transcription variant",
+          "pred" : "hasRelatedSynonym",
+          "val" : "assortment derived variation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:51:50Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-02T05:03:18Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rate_of_transcription_variant"
+      "lbl" : "assortment_derived_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001553",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001987",
       "meta" : {
         "definition" : {
-          "val" : "A functional variant that changes the translational product level with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A feature variant, where the alteration occurs downstream of the transcript termination site.",
+          "xrefs" : [ ]
         },
+        "comments" : [ "Requested by Graham Ritchie, EBI/Sanger." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translational product level variant",
+          "val" : "downstream transcript variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57426,24 +61309,24 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:53:32Z"
+          "val" : "2013-07-31T03:47:51Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translational_product_level_variant"
+      "lbl" : "downstream_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000222",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000656",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding lysyl tRNA (SO:0000265).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that can be transcribed into a small temporal RNA (stRNA). Found in roundworm development.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lysine tRNA primary transcript",
+          "val" : "stRNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57452,102 +61335,128 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lysine_tRNA_primary_transcript"
+      "lbl" : "stRNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000221",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001503",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding leucyl tRNA (SO:0000264).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A transcript for which no open reading frame has been identified and for which no other function has been determined.",
+          "xrefs" : [ "MGI:hdeen" ]
         },
+        "comments" : [ "Ensembl and Vega also use this term name. Requested by Howard Deen of MGI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "leucine tRNA primary transcript",
+          "val" : "processed transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-12-21T05:37:14Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "leucine_tRNA_primary_transcript"
+      "lbl" : "processed_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001552",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000659",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that decreases the rate of transcription with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that can be transcribed into a transfer-messenger RNA (tmRNA).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "decreased transcription rate variant",
+          "val" : "tmRNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:52:43Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "decreased_transcription_rate_variant"
+      "lbl" : "tmRNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#edited_from",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001506",
       "meta" : {
+        "definition" : {
+          "val" : "A collection of sequences (often chromosomes) of an individual.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "variant genome",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T02:19:45Z"
+          "val" : "2010-03-03T02:11:25Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "edited_from"
+      "type" : "CLASS",
+      "lbl" : "variant_genome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001548",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001505",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that increases transcript stability with respect to a reference sequence.",
+          "val" : "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "increased transcript stability variant",
+          "pred" : "hasRelatedSynonym",
+          "val" : "reference genome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:50:39Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-03T02:10:03Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "increased_transcript_stability_variant"
+      "lbl" : "reference_genome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000217",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000658",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding glutamyl tRNA (SO:0000260).",
+          "val" : "A repeat that is located at dispersed sites in the genome.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Interspersed_repeat"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "glutamine tRNA primary transcript",
+          "val" : "interspersed repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "dispersed repeat",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:dispersed",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57556,61 +61465,83 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "glutamine_tRNA_primary_transcript"
+      "lbl" : "dispersed_repeat"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001547",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001989",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that decreases transcript stability with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A 5' UTR variant where a premature start codon is lost.",
+          "xrefs" : [ "SANGER:am" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "decrease transcript stability variant",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:50:23Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2013-07-31T03:56:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "decreased_transcript_stability_variant"
+      "lbl" : "5_prime_UTR_premature_start_codon_loss_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000216",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001500",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding glutaminyl tRNA (SO:0000260).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus.",
+          "xrefs" : [ "JAX:hdene" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "glutamic acid tRNA primary transcript",
+          "val" : "phenotypic marker",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "heritable phenotypic marker",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-12-07T01:50:55Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "glutamic_acid_tRNA_primary_transcript"
+      "lbl" : "heritable_phenotypic_marker"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000219",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000653",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding histidyl tRNA (SO:0000262).",
+          "val" : "Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Renamed from rRNA_28S to cytosolic_28S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/28S_ribosomal_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histidine tRNA primary transcript",
+          "val" : "cytosolic 28S rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic rRNA 28S",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 28S ribosomal RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 28S LSU rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57619,17 +61550,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histidine_tRNA_primary_transcript"
+      "lbl" : "cytosolic_28S_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001549",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001984",
       "meta" : {
         "definition" : {
-          "val" : "A variant that changes alters the transcription of a transcript with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene cassette array that corresponds to a silenced version of a mating type region.",
+          "xrefs" : [ "PomBase:mah" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "transcription variant",
+          "pred" : "hasRelatedSynonym",
+          "val" : "silent mating-type cassette",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57640,21 +61571,38 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:51:26Z"
+          "val" : "2013-07-31T02:40:38Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcription_variant"
+      "lbl" : "silent_mating_type_cassette_array"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000218",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000652",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding glycyl tRNA (SO:0000263).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes.",
+          "xrefs" : [ "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001" ]
         },
+        "comments" : [ "Renamed from rRNA_5S to cytosolic_5S_rRNA on 27 May 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/5S_ribosomal_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "glycine tRNA primary transcript",
+          "val" : "cytosolic 5S ribosomal RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 5S rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic rRNA 5S",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic 5S LSU rRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57663,36 +61611,58 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "glycine_tRNA_primary_transcript"
+      "lbl" : "cytosolic_5S_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000213",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001983",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding asparaginyl tRNA (SO:0000256).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A 5' UTR variant where a premature start codon is introduced, moved or lost.",
+          "xrefs" : [ "SANGER:am" ]
         },
+        "comments" : [ "Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "asparagine tRNA primary transcript",
+          "val" : "5' UTR premature start codon variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T04:36:25Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "asparagine_tRNA_primary_transcript"
+      "lbl" : "5_prime_UTR_premature_start_codon_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000697",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000655",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a transcript with stop codon readthrough.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://www.gencodegenes.org/gencode_biotypes.html"
+        }, {
+          "val" : "http://en.wikipedia.org/wiki/NcRNA"
+        } ],
         "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_qualifier:other",
+          "xrefs" : [ ]
+        }, {
           "pred" : "hasExactSynonym",
-          "val" : "gene with stop codon read through",
+          "val" : "noncoding RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "known_ncrna",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57701,65 +61671,73 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_stop_codon_read_through"
+      "lbl" : "ncRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001544",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001502",
       "meta" : {
         "definition" : {
-          "val" : "A transcript processing variant whereby the process of editing is disrupted with respect to the reference.",
+          "val" : "An experimental feature with high sequence identity to another sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by tracker ID: 2902685." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "editing variant",
+          "val" : "high identity region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:49:25Z"
+          "val" : "2009-12-11T11:06:05Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "editing_variant"
+      "lbl" : "high_identity_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000212",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001986",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding arginyl tRNA (SO:0000255).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A feature variant, where the alteration occurs upstream of the transcript TSS.",
+          "xrefs" : [ "EBI:gr" ]
         },
+        "comments" : [ "Requested by Graham Ritchie, EBI/Sanger." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "arginine tRNA primary transcript",
+          "val" : "upstream transcript variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-31T03:46:14Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "arginine_tRNA_primary_transcript"
+      "lbl" : "upstream_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000696",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000654",
       "meta" : {
         "definition" : {
-          "val" : "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A mitochondrial gene located in a maxicircle.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Oligonucleotide"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "oligonucleotide",
+          "val" : "maxi-circle gene",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "maxicircle gene",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57768,17 +61746,18 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "oligo"
+      "lbl" : "maxicircle_gene"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001543",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001985",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication.",
+          "xrefs" : [ "ISBN:0805350152" ]
         },
+        "comments" : [ "Requested by Midori Harris, 2013." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript processing variant",
+          "val" : "Okazaki fragment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57786,95 +61765,119 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:48:48Z"
+          "val" : "2013-07-31T02:57:55Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_processing_variant"
+      "lbl" : "Okazaki_fragment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000215",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001501",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding cysteinyl tRNA (SO:0000258).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A collection of peptide sequences.",
+          "xrefs" : [ "BBOP:nlw" ]
         },
+        "comments" : [ "Term requested via tracker ID: 2910829." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cysteine tRNA primary transcript",
+          "val" : "peptide set",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "peptide collection",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-12-11T10:58:58Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cysteine_tRNA_primary_transcript"
+      "lbl" : "peptide_collection"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000699",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001980",
       "meta" : {
         "definition" : {
-          "val" : "A sequence_feature with an extent of zero.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a.",
+          "xrefs" : [ "PMID:19249238", "PMID:8571452", "SO:ml" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "comments" : [ "A plant specific region." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "boundary",
+          "val" : "GBF binding sequence",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "breakpoint",
+          "val" : "G-box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A junction is a boundary between regions. A boundary has an extent of zero."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T04:00:50Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "junction"
+      "lbl" : "G_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001546",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001982",
       "meta" : {
         "definition" : {
-          "val" : "A variant that changes the stability of a transcript with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core).",
+          "xrefs" : [ "PMID:2347304", "PMID:2902624", "SO:ml" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript stability variant",
+          "val" : "I-box promoter motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:50:01Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T04:17:55Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_stability_variant"
+      "lbl" : "I-box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000698",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000651",
       "meta" : {
         "definition" : {
-          "val" : "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with stop codon redefined as pyrrolysine",
+          "val" : "cytosolic LSU rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic large subunit rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic LSU RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57883,22 +61886,55 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_stop_codon_redefined_as_pyrrolysine"
+      "lbl" : "cytosolic_LSU_rRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001545",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000650",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes polyadenylation with respect to a reference sequence.",
+          "val" : "Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Renamed to cytosolic_SSU_rRNA from small_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polyadenylation variant",
+          "val" : "cytosolic SSU ribosomal RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic small subunit rRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "cytosolic SSU rRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "cytosolic_SSU_rRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001981",
+      "meta" : {
+        "definition" : {
+          "val" : "An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants.",
+          "xrefs" : [ "PMID:17381552", "PMID:2902624", "SO:ml" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "L-box promoter element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "L-box",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:49:40Z"
+          "val" : "2013-07-30T04:12:19Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -57908,17 +61944,64 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polyadenylation_variant"
+      "lbl" : "L_box"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000214",
+      "id" : "http://purl.obolibrary.org/obo/so#RNAMOD",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasScope",
+          "val" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"
+        } ]
+      },
+      "lbl" : "RNA modification"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000649",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000276"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00246",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001090"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000646",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding aspartyl tRNA (SO:0000257).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules.",
+          "xrefs" : [ "PMID:12592000" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/SiRNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "aspartic acid tRNA primary transcript",
+          "val" : "INSDC_qualifier:siRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small interfering RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57927,61 +62010,69 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "aspartic_acid_tRNA_primary_transcript"
+      "lbl" : "siRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001540",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001977",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which alters the level of a transcript.",
+          "val" : "A region of a transcript encoding the cleavage site for a ribonuclease enzyme.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "level of transcript variant",
+          "val" : "ribonuclease site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:47:07Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2013-07-30T11:41:06Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "level_of_transcript_variant"
+      "lbl" : "ribonuclease_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000693",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001976",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes an mRNA that is recoded.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with recoded mRNA",
+          "val" : "three prime sticky end restriction enzyme cleavage site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T11:37:19Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_recoded_mRNA"
+      "lbl" : "three_prime_sticky_end_restriction_enzyme_cleavage_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000692",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000645",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a dicistronic transcript.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "The reverse complement of the primary transcript.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with dicistronic transcript",
+          "val" : "antisense primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -57990,105 +62081,148 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_dicistronic_transcript"
+      "lbl" : "antisense_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000211",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000648",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000647"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001979",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding alanyl tRNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A motif that affects the stability of RNA.",
+          "xrefs" : [ "PMID:22495308", "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "alanine tRNA primary transcript",
+          "val" : "RNA stability element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T03:33:53Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alanine_tRNA_primary_transcript"
+      "lbl" : "RNA_stability_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000695",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000647",
       "meta" : {
         "definition" : {
-          "val" : "A sequence used in experiment.",
+          "val" : "A primary transcript encoding a micro RNA.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "micro RNA primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stRNA primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "small temporal RNA primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "miRNA primary transcript",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stRNA_primary_transcript",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Requested by Lynn Crosby, jan 2006."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0000648"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "reagent"
+      "lbl" : "miRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001542",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001978",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.",
+          "val" : "A region of sequence where developer information is encoded.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Jackie Quinn for use in synthetic biology." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "increased transcript level variant",
+          "val" : "DNA signature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:48:17Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "val" : "2013-07-30T11:49:22Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "increased_transcript_level_variant"
+      "lbl" : "signature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001541",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001973",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A histone 3 modification where the modification is the acetylation of the residue.",
+          "xrefs" : [ "EBI:nj", "ISBN:0815341059", "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "decreased transcript level",
+          "val" : "histone 3 acetylation site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "H3ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T10:46:42Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:47:47Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "decreased_transcript_level_variant"
+      "lbl" : "histone_3_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000694",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000642",
       "meta" : {
         "definition" : {
-          "val" : "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.",
-          "xrefs" : [ "SO:cb" ]
+          "val" : "A region that can be transcribed into a signal recognition particle RNA (SRP RNA).",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "single nucleotide polymorphism",
+          "val" : "SRP RNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58097,17 +62231,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SNP"
+      "lbl" : "SRP_RNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000210",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000641",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a transfer RNA (SO:0000253).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region of a repeating tetranucleotide sequence (four bases).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tRNA primary transcript",
+          "val" : "tetranucleotide repeat microsatellite feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58116,72 +62250,84 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tRNA_primary_transcript"
+      "lbl" : "tetranucleotide_repeat_microsatellite_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000691",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001972",
       "meta" : {
         "definition" : {
-          "val" : "The initiator methionine that has been cleaved from a mature polypeptide sequence.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A histone 4 modification where the modification is the acetylation of the residue.",
+          "xrefs" : [ "EBI:nj", "ISBN:0815341059", "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cleaved initiator methionine",
+          "val" : "histone 4 acetylation site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "init_met",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "initiator methionine",
+          "pred" : "hasExactSynonym",
+          "val" : "H4ac",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00067"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T10:43:04Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cleaved_initiator_methionine"
+      "lbl" : "histone_4_acetylation_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000690",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001975",
       "meta" : {
         "definition" : {
-          "val" : "A gene that encodes a polycistronic transcript.",
-          "xrefs" : [ "SO:xp" ]
+          "val" : "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "gene with polycistronic transcript",
+          "val" : "five prime sticky end restriction enzyme cleavage site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T11:32:16Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_with_polycistronic_transcript"
+      "lbl" : "five_prime_sticky_end_restriction_enzyme_cleavage_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000209",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000644",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a ribosomal RNA.",
+          "val" : "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.",
           "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Antisense_RNA"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "ribosomal RNA primary transcript",
+          "val" : "antisense RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:ncRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA primary transcript",
+          "val" : "INSDC_qualifier:antisense_RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58190,84 +62336,88 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_primary_transcript"
+      "lbl" : "antisense_RNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001537",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000643",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes one or more sequence features.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp.",
+          "xrefs" : [ "http://www.informatics.jax.org/silver/glossary.shtml" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://vat.gersteinlab.org/formats.php"
+          "val" : "http://en.wikipedia.org/wiki/Minisatellite"
         } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "structural variant",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:repeat_region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAT:svOverlap",
-          "xrefs" : [ ]
+          "val" : "VNTR",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/books/NBK21126/def-item/A9655/" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:structural_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "INSDC_qualifier:minisatellite",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:31:01Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "structural_variant"
+      "lbl" : "minisatellite"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000206",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001974",
       "meta" : {
         "definition" : {
-          "val" : "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor.",
+          "xrefs" : [ "EBI:nj" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "SINE element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Short interspersed element",
+          "val" : "CTCF binding site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Short interspersed nuclear element",
+          "val" : "CCCTF binding site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2013-07-30T10:59:11Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "SINE_element"
+      "lbl" : "CTCF_binding_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000689",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000682",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS",
+      "lbl" : "splicing_feature"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000681",
       "meta" : {
         "definition" : {
-          "val" : "A match against cDNA sequence.",
+          "val" : "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cDNA match",
+          "val" : "aberrant processed transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58276,54 +62426,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cDNA_match"
+      "lbl" : "aberrant_processed_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001536",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000200",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant in which the function of a gene product is altered with respect to a reference.",
+          "val" : "The 5' most coding exon.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "functional variant",
+          "val" : "five prime coding exon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "5' coding exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:30:25Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "functional_variant"
+      "lbl" : "five_prime_coding_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000205",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000684",
       "meta" : {
         "definition" : {
-          "val" : "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A region of nucleotide sequence targeted by a nuclease enzyme.",
+          "xrefs" : [ "SO:ma" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Three_prime_untranslated_region"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "three prime untranslated region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:3'UTR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "three prime UTR",
+          "val" : "nuclease sensitive site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58332,101 +62470,101 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_UTR"
+      "lbl" : "nuclease_sensitive_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000208",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001531",
       "meta" : {
         "definition" : {
-          "val" : "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.",
-          "xrefs" : [ "http://www.genetics.org/cgi/reprint/156/4/1983.pdf" ]
+          "val" : "A polypeptide region that targets a polypeptide to he cytoplasm.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Nuclear_export_signal"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "terminal inverted repeat element",
+          "val" : "nuclear export signal",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "TIR element",
+          "val" : "NES",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-11T02:25:25Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "terminal_inverted_repeat_element"
+      "lbl" : "nuclear_export_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001539",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001530",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that affects the functioning of a translational product with respect to a reference sequence.",
+          "val" : "A polypeptide region that targets a polypeptide to the lysosome.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "translational product variant",
+          "val" : "lysosomal localization signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:46:15Z"
+          "val" : "2010-03-11T02:24:10Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translational_product_function_variant"
+      "lbl" : "lysosomal_localization_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001538",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000683",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which alters the functioning of a transcript with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron.",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript function variant",
+          "val" : "exonic splice enhancer",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:32:58Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_function_variant"
+      "lbl" : "exonic_splice_enhancer"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000207",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000680",
       "meta" : {
         "definition" : {
-          "val" : "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ.",
+          "val" : "A start codon that is not the usual AUG sequence.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "SSLP",
+          "pred" : "hasExactSynonym",
+          "val" : "non ATG start codon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "simple sequence length variation",
+          "val" : "non canonical start codon",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "simple sequence length polymorphism",
+          "pred" : "hasExactSynonym",
+          "val" : "non-canonical start codon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58435,50 +62573,115 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "simple_sequence_length_variation"
+      "lbl" : "non_canonical_start_codon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001533",
+      "id" : "http://purl.obolibrary.org/obo/BS_00210",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001109"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00214",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001137"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001529",
       "meta" : {
         "definition" : {
-          "val" : "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.",
+          "val" : "A polypeptide region that targets a polypeptide to the endosome.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cryptic splice site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "cryptic splice signal",
+          "val" : "endosomal localization signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T03:25:06Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-11T02:20:58Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cryptic_splice_site"
+      "lbl" : "endosomal_localization_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000202",
+      "id" : "http://purl.obolibrary.org/obo/BS_00213",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001135"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00212",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001133"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00211",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001110"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000679",
       "meta" : {
         "definition" : {
-          "val" : "The coding exon that is most 3-prime on a given transcript.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A 5' splice site which does not have the sequence \"GT\".",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "3' coding exon",
+          "pred" : "hasExactSynonym",
+          "val" : "non canonical 5' splice site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "three prime coding exon",
+          "val" : "non-canonical five prime splice site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non canonical five prime splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58487,48 +62690,50 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "three_prime_coding_exon"
+      "lbl" : "non_canonical_five_prime_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000686",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001526",
       "meta" : {
         "definition" : {
-          "val" : "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "translocation element",
+          "pred" : "hasRelatedSynonym",
+          "val" : "base call error correction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-09T02:18:07Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "translocation_element"
+      "lbl" : "base_call_error_correction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000685",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000678",
       "meta" : {
         "definition" : {
-          "val" : "DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I.",
-          "xrefs" : [ ]
+          "val" : "A 3' splice site that does not have the sequence \"AG\".",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "DHS",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_qualifier:DNAseI_hypersensitive_site",
+          "val" : "non canonical three prime splice site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "DNAseI hypersensitive site",
+          "val" : "non-canonical three prime splice site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_feature:regulatory",
+          "pred" : "hasRelatedSynonym",
+          "val" : "non canonical 3' splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58537,212 +62742,251 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "DNAseI_hypersensitive_site"
+      "lbl" : "non_canonical_three_prime_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001532",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001525",
       "meta" : {
         "definition" : {
-          "val" : "A region recognized by a recombinase.",
+          "val" : "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Recombination_Signal_Sequences"
-        } ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "recombination signal sequence",
+          "val" : "assembly error correction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T03:16:47Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-09T02:16:31Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "recombination_signal_sequence"
+      "lbl" : "assembly_error_correction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000201",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001528",
       "meta" : {
         "definition" : {
-          "val" : "An exon that is bounded by 5' and 3' splice sites.",
-          "xrefs" : [ "PMID:10373547" ]
+          "val" : "A polypeptide region that targets a polypeptide to the nucleus.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Nuclear_localization_signal"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "interior exon",
+          "val" : "NLS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-11T02:16:38Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "interior_exon"
+      "lbl" : "nuclear_localization_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000204",
+      "id" : "http://purl.obolibrary.org/obo/BS_00216",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001136"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00215",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001134"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001527",
       "meta" : {
         "definition" : {
-          "val" : "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.",
-          "xrefs" : [ "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "A region of peptide sequence used to target the polypeptide molecule to a specific organelle.",
+          "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/5'_UTR"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "5' UTR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five_prime_untranslated_region",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "five prime UTR",
+          "val" : "peptide localization signal",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:5'UTR",
+          "pred" : "hasRelatedSynonym",
+          "val" : "localization signal",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-11T02:15:05Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "five_prime_UTR"
+      "lbl" : "peptide_localization_signal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001535",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001522",
       "meta" : {
         "definition" : {
-          "val" : "A P_element is a DNA transposon responsible for hybrid dysgenesis.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "P element",
+          "val" : "When a translocation is simply moving genetic material from one chromosome to another.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-12T03:40:33Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:59:51Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "p_element"
+      "lbl" : "insertional"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000688",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000675",
       "meta" : {
         "definition" : {
-          "val" : "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.",
-          "xrefs" : [ "SO:ls" ]
+          "val" : "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "golden path",
+          "val" : "canonical splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0000677"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0000676"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "golden_path"
+      "lbl" : "canonical_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000203",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000674",
       "meta" : {
         "definition" : {
-          "val" : "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.",
+          "val" : "A splice site where the donor and acceptor sites differ from the canonical form.",
           "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "untranslated region",
+          "val" : "non-canonical splice site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non canonical splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0000679"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#consider",
+          "val" : "SO:0000678"
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "UTR"
+      "lbl" : "non_canonical_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001534",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001521",
       "meta" : {
         "definition" : {
-          "val" : "A polypeptide region that targets a polypeptide to the nuclear rim.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "xrefs" : [ {
-          "val" : "PMID:16027110"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "nuclear rim localization signal",
+          "val" : "When translocation occurs between nonhomologous chromosomes and involved an equal exchange of genetic materials.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-11T03:31:30Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2010-03-04T02:59:34Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "nuclear_rim_localization_signal"
+      "lbl" : "reciprocal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000687",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001524",
       "meta" : {
         "definition" : {
-          "val" : "The space between two bases in a sequence which marks the position where a deletion has occurred.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "When a genome contains an abnormal amount of chromosomes.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "deletion junction",
+          "pred" : "hasRelatedSynonym",
+          "val" : "chromosomally aberrant genome",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-05T02:21:00Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "deletion_junction"
+      "lbl" : "chromosomally_aberrant_genome"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000242",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000677",
       "meta" : {
         "definition" : {
-          "val" : "The untranslated sequence separating the 'cistrons' of multicistronic mRNA.",
+          "val" : "The canonical 5' splice site has the sequence \"GT\".",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "untranslated region polycistronic mRNA",
+          "val" : "canonical 5' splice site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "canonical five prime splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -58751,249 +62995,165 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "untranslated_region_polycistronic_mRNA"
+      "lbl" : "canonical_five_prime_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001573",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000676",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "The canonical 3' splice site has the sequence \"AG\".",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "intron gain variant",
+          "val" : "canonical three prime splice site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "intron gain",
+          "val" : "canonical 3' splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:31:25Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "intron_gain_variant"
+      "lbl" : "canonical_three_prime_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000241",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001523",
       "meta" : {
         "definition" : {
-          "val" : "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.",
-          "xrefs" : [ "SO:cjm" ]
+          "val" : "An attribute of a duplication, which is an insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "internal UTR",
+          "pred" : "hasRelatedSynonym",
+          "val" : "duplication attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-05T01:56:33Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "internal_UTR"
+      "lbl" : "duplication_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001572",
+      "id" : "http://purl.obolibrary.org/obo/BS_00219",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001138"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000671",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby an exon is lost from the transcript.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence eliminated from the genome of ciliates during nuclear differentiation.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "exon loss",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:exon_loss_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:EXON_DELETED",
+          "val" : "internal eliminated sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:31:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "exon_loss_variant"
+      "lbl" : "internal_eliminated_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000244",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000670",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation.",
+          "xrefs" : [ "SO:ma" ]
+        },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "four-cutter_restriction_sit",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "4-cutter_restriction_site",
+          "pred" : "hasExactSynonym",
+          "val" : "chromosome breakage sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "four_cutter_restriction_site"
+      "lbl" : "chromosome_breakage_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001575",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001520",
       "meta" : {
         "definition" : {
-          "val" : "A splice variant that changes the 2 base pair region at the 5' end of an intron.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An attribute of a translocation, which is then a region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.",
+          "xrefs" : [ ]
         },
-        "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "splice donor variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:splice_donor_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:splice-donor",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:splice_donor_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:splice_donor_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:SPLICE_SITE_DONOR",
+          "val" : "translocation attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:58:47Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:32:10Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_donor_variant"
+      "lbl" : "translocaton_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001574",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000673",
       "meta" : {
         "definition" : {
-          "val" : "A splice variant that changes the 2 base region at the 3' end of an intron.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "An RNA synthesized on a DNA or RNA template by an RNA polymerase.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "comments" : [ "Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+          "val" : "http://en.wikipedia.org/wiki/RNA"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:SPLICE_SITE_ACCEPTOR",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:splice_acceptor_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:splice_acceptor_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:splice-acceptor",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:splice_acceptor_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "splice acceptor variant",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:misc_RNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:31:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splice_acceptor_variant"
+      "lbl" : "transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000243",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000672",
       "meta" : {
         "definition" : {
-          "val" : "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Internal_ribosome_entry_site"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "internal ribosomal entry site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "IRES",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "internal ribosomal entry sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "internal ribosome entry sequence",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "internal ribosome entry site",
+          "val" : "macronucleus destined segment",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59002,59 +63162,73 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "internal_ribosome_entry_site"
+      "lbl" : "macronucleus_destined_segment"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000240",
+      "id" : "http://purl.obolibrary.org/obo/BS_00221",
       "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "chromosome variation",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001140"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00220",
+      "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001139"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "chromosome_variation"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001571",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001519",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby a new splice site is created due to the activation of a new donor.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "cryptic splice donor",
+          "val" : "An inversion event that does not include the centromere.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:58:35Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:30:35Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cryptic_splice_donor"
+      "lbl" : "paracentric"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001570",
+      "id" : "http://purl.obolibrary.org/obo/BS_00225",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001122"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001518",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby a new splice site is created due to the activation of a new acceptor.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "cryptic splice acceptor",
+          "val" : "An inversion event that includes the centromere.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
@@ -59063,71 +63237,60 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:30:11Z"
+          "val" : "2010-03-04T02:58:24Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cryptic_splice_acceptor"
+      "lbl" : "pericentric"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000239",
+      "id" : "http://purl.obolibrary.org/obo/BS_00224",
       "meta" : {
-        "definition" : {
-          "val" : "The sequences extending on either side of a specific region.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "flanking region",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001121"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "flanking_region"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000238",
+      "id" : "http://purl.obolibrary.org/obo/BS_00223",
       "meta" : {
-        "definition" : {
-          "val" : "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.",
-          "xrefs" : [ "http://www.genetics.org/cgi/reprint/156/4/1983.pdf" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "foldback element",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "LVR element",
-          "xrefs" : [ ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001120"
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "long inverted repeat element",
-          "xrefs" : [ ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00222",
+      "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001115"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
       },
-      "type" : "CLASS",
-      "lbl" : "foldback_element"
+      "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001569",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001999",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant causing a new (functional) splice site.",
-          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+          "val" : "DNA motif that is a component of a mating type region.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cryptic splice site activation",
+          "val" : "mating type region motif",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59135,78 +63298,58 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:29:41Z"
+          "val" : "2014-01-05T07:30:17Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cryptic_splice_site_variant"
+      "lbl" : "mating_type_region_motif"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001566",
+      "id" : "http://purl.obolibrary.org/obo/BS_00229",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001126"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001515",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant located within a regulatory region.",
+          "val" : "A quality of an insertion where the insert is in a cytologically inverted orientation.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:regulatory_region_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "regulatory region variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:regulatory_region_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:REGULATION",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "regulatory_region_",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Regulatory region variations - In regulatory region annotated by Ensembl."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:57:40Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:28:48Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "regulatory_region_variant"
+      "lbl" : "inverted"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000235",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000668",
       "meta" : {
         "definition" : {
-          "val" : "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667].",
+          "val" : "A match against an EST sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcription factor binding site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "TF binding site",
+          "val" : "EST match",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59215,221 +63358,273 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "TF_binding_site"
+      "lbl" : "EST_match"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000234",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000667",
       "meta" : {
         "definition" : {
-          "val" : "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.",
-          "xrefs" : [ "SO:ma" ]
+          "val" : "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA", "http://purl.obolibrary.org/obo/so#DBVAR" ],
         "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/MRNA"
-        }, {
-          "val" : "http://www.gencodegenes.org/gencode_biotypes.html"
+          "val" : "loinc:LA6687-3"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:mRNA",
-          "xrefs" : [ ]
+          "val" : "insertion",
+          "xrefs" : [ "http://www.ncbi.nlm.nih.gov/dbvar/" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#dbvar"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "messenger RNA",
+          "val" : "nucleotide insertion",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "protein_coding_transcript",
+          "val" : "nucleotide_insertion",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:1000034"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mRNA"
+      "lbl" : "insertion"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001565",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001514",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby a two genes have become joined.",
+          "val" : "A quality of an insertion where the insert is not in a cytologically inverted orientation.",
           "xrefs" : [ "SO:ke" ]
         },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "gene fusion",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:28:28Z"
+          "val" : "2010-03-04T02:56:49Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_fusion"
+      "lbl" : "direct"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001568",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001998",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the process of splicing.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method.",
+          "xrefs" : [ "PMID:23934893" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "splicing variant",
+          "pred" : "hasRelatedSynonym",
+          "val" : "guide RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "gRNA",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:splicing_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "small guide RNA",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:29:22Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2014-01-05T07:25:08Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "splicing_variant"
+      "lbl" : "sgRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000237",
+      "id" : "http://purl.obolibrary.org/obo/BS_00228",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001124"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001517",
       "meta" : {
+        "definition" : {
+          "val" : "When a region of a chromosome is changed to the reverse order without duplication or deletion.",
+          "xrefs" : [ ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript attribute",
+          "val" : "inversion attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:58:10Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_attribute"
+      "lbl" : "inversion_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001567",
+      "id" : "http://purl.obolibrary.org/obo/BS_00227",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001125"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001516",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.",
+          "val" : "The quality of a duplication where the new region exists independently of the original.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "stop retained variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:SYNONYMOUS_STOP",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:stop_retained_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:57:51Z"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:NON_SYNONYMOUS_STOP",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:stop_retained_variant",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "free"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00226",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001123"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:stop_retained_variant",
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000669",
+      "meta" : {
+        "definition" : {
+          "val" : "A feature where a segment of DNA has been rearranged from what it was in the parent cell.",
           "xrefs" : [ ]
-        }, {
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VAAST:stop_retained",
+          "val" : "sequence rearrangement feature",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-04-19T05:02:30Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stop_retained_variant"
+      "lbl" : "sequence_rearrangement_feature"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000236",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000664",
       "meta" : {
         "definition" : {
-          "val" : "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.",
-          "xrefs" : [ "SGD:rb", "SO:ma" ]
+          "val" : "A region of a chromosome that has been introduced by backcrossing with a separate species.",
+          "xrefs" : [ "PMID:11454782" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "open reading frame",
+          "val" : "introgressed chromosome region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "introgressed_chromosome_region"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001511",
+      "meta" : {
+        "definition" : {
+          "val" : "A change in chromosomes that occurs between two sections of the same chromosome or between homologous chromosomes.",
+          "xrefs" : [ ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:55:43Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "ORF"
+      "lbl" : "interchromosomal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000231",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001995",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a small nuclear RNA (SO:0000274).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence variant occurring in the intron, within 10 bases of exon.",
+          "xrefs" : [ "sanger:am" ]
         },
+        "comments" : [ "Added by Andy Menzies (Sanger)." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snRNA primary transcript",
+          "val" : "extended intronic splice region variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-01-04T06:37:27Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "snRNA_primary_transcript"
+      "lbl" : "extended_intronic_splice_region_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001562",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001994",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron.",
+          "xrefs" : [ "SANGER:am" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide post translational processing variant",
+          "val" : "intron base 5",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59437,38 +63632,44 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:59:06Z"
+          "val" : "2014-01-04T06:26:02Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_post_translational_processing_variant"
+      "lbl" : "intron_base_5"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#partial_evidence_for_feature",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001510",
       "meta" : {
         "definition" : {
-          "val" : "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A change in chromosomes that occurs between two separate chromosomes.",
+          "xrefs" : [ ]
         },
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-04T02:55:25Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "partial_evidence_for_feature"
+      "type" : "CLASS",
+      "lbl" : "intrachromosomal"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000230",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000663",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding valyl tRNA (SO:000273).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region that can be transcribed into a transfer RNA (tRNA).",
+          "xrefs" : [ ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "valine tRNA primary transcript",
+          "val" : "tRNA encoding",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59477,108 +63678,76 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "valine_tRNA_primary_transcript"
+      "lbl" : "tRNA_encoding"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001561",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000666",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.",
+          "val" : "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide partial loss of function",
+          "val" : "mobile intron",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:58:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_partial_loss_of_function"
+      "lbl" : "mobile_intron"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000233",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001997",
       "meta" : {
         "definition" : {
-          "val" : "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed.",
+          "xrefs" : [ "POMBE:al" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Mature_transcript"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "mature transcript",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-01-05T07:02:01Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "A processed transcript cannot contain introns."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mature_transcript"
+      "lbl" : "subtelomere"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001564",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001513",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where the structure of the gene is changed.",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "xrefs" : [ {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:GENE",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:gene_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "gene structure variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:gene_variant",
+          "val" : "An insertion of extension of a tandem repeat.",
           "xrefs" : [ ]
-        } ],
+        },
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:28:01Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2010-03-04T02:56:37Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "gene_variant"
+      "lbl" : "tandem"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001563",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001512",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where copies of a feature (CNV) are either increased or decreased.",
+          "val" : "A quality of a chromosomal insertion,.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "copy number change",
+          "val" : "insertion attribute",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59586,24 +63755,24 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:27:33Z"
+          "val" : "2010-03-04T02:55:56Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "copy_number_change"
+      "lbl" : "insertion_attribute"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000232",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000665",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a small nucleolar mRNA (SO:0000275).",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A transcript that is monocistronic.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snoRNA primary transcript",
+          "val" : "monocistronic transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59612,67 +63781,67 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "snoRNA_primary_transcript"
+      "lbl" : "monocistronic_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001560",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001996",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "Region of intronic sequence within 10 bases of an exon.",
+          "xrefs" : [ "SANGER:am" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "inactive ligand binding site",
+          "val" : "extended intronic splice region ",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2014-01-04T06:41:23Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:58:00Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "inactive_ligand_binding_site"
+      "lbl" : "extended_intronic_splice_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001559",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001551",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.",
+          "val" : "A sequence variant that increases the rate of transcription with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide loss of function variant",
+          "val" : "increased transcription rate variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:56:58Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:52:17Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_loss_of_function_variant"
+      "lbl" : "increased_transcription_rate_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000228",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000220",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding tryptophanyl tRNA (SO:000271).",
+          "val" : "A primary transcript encoding isoleucyl tRNA (SO:0000263).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tryptophan tRNA primary transcript",
+          "val" : "isoleucine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59681,33 +63850,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tryptophan_tRNA_primary_transcript"
+      "lbl" : "isoleucine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#trans_spliced_to",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001550",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that changes the rate of transcription with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "rate of transcription variant",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T02:22:00Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:51:50Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "trans_spliced_to"
+      "type" : "CLASS",
+      "lbl" : "rate_of_transcription_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000227",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000222",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding threonyl tRNA (SO:000270).",
+          "val" : "A primary transcript encoding lysyl tRNA (SO:0000265).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "threonine tRNA primary transcript",
+          "val" : "lysine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59716,42 +63894,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "threonine_tRNA_primary_transcript"
+      "lbl" : "lysine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001558",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001553",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.",
+          "val" : "A functional variant that changes the translational product level with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide localization variant",
+          "val" : "translational product level variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:56:37Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:53:32Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_localization_variant"
+      "lbl" : "translational_product_level_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000229",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000221",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding tyrosyl tRNA (SO:000272).",
+          "val" : "A primary transcript encoding leucyl tRNA (SO:0000264).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "tyrosine tRNA primary transcript",
+          "val" : "leucine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59760,105 +63938,102 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tyrosine_tRNA_primary_transcript"
+      "lbl" : "leucine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001555",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001552",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which decreases the translational product level with respect to a reference sequence.",
+          "val" : "A sequence variant that decreases the rate of transcription with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "decrease translational product level",
+          "val" : "decreased transcription rate variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:54:25Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:52:43Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "decreased_translational_product_level"
+      "lbl" : "decreased_transcription_rate_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000224",
+      "id" : "http://purl.obolibrary.org/obo/so#edited_from",
       "meta" : {
-        "definition" : {
-          "val" : "A primary transcript encoding phenylalanyl tRNA (SO:0000267).",
-          "xrefs" : [ "SO:ke" ]
-        },
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "phenylalanine tRNA primary transcript",
-          "xrefs" : [ ]
-        } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2009-08-19T02:19:45Z"
         } ]
       },
-      "type" : "CLASS",
-      "lbl" : "phenylalanine_tRNA_primary_transcript"
+      "type" : "PROPERTY",
+      "lbl" : "edited_from"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000223",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001548",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding methionyl tRNA (SO:0000266).",
+          "val" : "A sequence variant that increases transcript stability with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "methionine tRNA primary transcript",
+          "val" : "increased transcript stability variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:50:39Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "methionine_tRNA_primary_transcript"
+      "lbl" : "increased_transcript_stability_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001554",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000217",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which changes polypeptide functioning with respect to a reference sequence.",
+          "val" : "A primary transcript encoding glutamyl tRNA (SO:0000260).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide function variant",
+          "val" : "glutamine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:53:54Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_function_variant"
+      "lbl" : "glutamine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000226",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000216",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding seryl tRNA (SO:000269).",
+          "val" : "A primary transcript encoding glutaminyl tRNA (SO:0000260).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "serine tRNA primary transcript",
+          "val" : "glutamic acid tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59867,17 +64042,17 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "serine_tRNA_primary_transcript"
+      "lbl" : "glutamic_acid_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001557",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001547",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which causes gain of polypeptide function with respect to a reference sequence.",
+          "val" : "A sequence variant that decreases transcript stability with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide gain of function variant",
+          "val" : "decrease transcript stability variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59885,24 +64060,24 @@
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:56:12Z"
+          "val" : "2010-03-22T11:50:23Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_gain_of_function_variant"
+      "lbl" : "decreased_transcript_stability_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000225",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000219",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding prolyl tRNA (SO:0000268).",
+          "val" : "A primary transcript encoding histidyl tRNA (SO:0000262).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "proline tRNA primary transcript",
+          "val" : "histidine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -59911,131 +64086,86 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "proline_tRNA_primary_transcript"
+      "lbl" : "histidine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001556",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000218",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which increases the translational product level with respect to a reference sequence.",
+          "val" : "A primary transcript encoding glycyl tRNA (SO:0000263).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "increase translational product level",
+          "val" : "glycine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T11:55:25Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "increased_translational_product_level"
+      "lbl" : "glycine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000264",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001549",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.",
+          "val" : "A variant that changes alters the transcription of a transcript with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "leucyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "leucyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "leucyl tRNA",
+          "val" : "transcription variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "leucyl_tRNA"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001595",
-      "meta" : {
-        "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "plus 2 frameshift variant",
-          "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "+2 frameshift variant",
-          "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:42:23Z"
+          "val" : "2010-03-22T11:51:26Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plus_2_frameshift_variant"
+      "lbl" : "transcription_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001111",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001544",
       "meta" : {
         "definition" : {
-          "val" : "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.",
-          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+          "val" : "A transcript processing variant whereby the process of editing is disrupted with respect to the reference.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Beta_sheet"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "strand",
-          "xrefs" : [ "uniprot:feature_type" ]
+          "pred" : "hasExactSynonym",
+          "val" : "editing variant",
+          "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:49:25Z"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00042"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_strand"
+      "lbl" : "editing_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000263",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000697",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that encodes a transcript with stop codon readthrough.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "isoleucyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "isoleucyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "isoleucyl-transfer ribonucleic acid",
+          "val" : "gene with stop codon read through",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60044,77 +64174,59 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "isoleucyl_tRNA"
+      "lbl" : "gene_with_stop_codon_read_through"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001110",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000213",
       "meta" : {
         "definition" : {
-          "val" : "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A primary transcript encoding asparaginyl tRNA (SO:0000256).",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta bulge loop six",
+          "val" : "asparagine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00211"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_bulge_loop_six"
+      "lbl" : "asparagine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001594",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000696",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.",
-          "xrefs" : [ "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535" ]
+          "val" : "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded.",
+          "xrefs" : [ "SO:ma" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Oligonucleotide"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "plus 1 frameshift variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "+1 frameshift variant",
+          "val" : "oligonucleotide",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:42:06Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "plus_1_frameshift_variant"
+      "lbl" : "oligo"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000266",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000212",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.",
+          "val" : "A primary transcript encoding arginyl tRNA (SO:0000255).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "methionyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "methionyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "methionyl-transfer RNA",
+          "val" : "arginine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60123,43 +64235,42 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "methionyl_tRNA"
+      "lbl" : "arginine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001113",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001543",
       "meta" : {
         "definition" : {
-          "val" : "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.",
-          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+          "val" : "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "parallel beta strand",
+          "val" : "transcript processing variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:48:48Z"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00151"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "parallel_beta_strand"
+      "lbl" : "transcript_processing_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001597",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001546",
       "meta" : {
         "definition" : {
-          "val" : "A secondary structure variant that compensate for the change made by a previous variant.",
+          "val" : "A variant that changes the stability of a transcript with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "compensatory transcript secondary structure variant",
+          "val" : "transcript stability variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60167,57 +64278,49 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:43:54Z"
+          "val" : "2010-03-22T11:50:01Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "compensatory_transcript_secondary_structure_variant"
+      "lbl" : "transcript_stability_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001596",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000699",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant within a transcript that changes the secondary structure of the RNA product.",
+          "val" : "A sequence_feature with an extent of zero.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "A junction is a boundary between regions. A boundary has an extent of zero." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript secondary structure variant",
+          "val" : "breakpoint",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "boundary",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:43:18Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_secondary_structure_variant"
+      "lbl" : "junction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000265",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000215",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.",
+          "val" : "A primary transcript encoding cysteinyl tRNA (SO:0000258).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "lysyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "lysyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "lysyl-transfer ribonucleic acid",
+          "val" : "cysteine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60226,180 +64329,124 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "lysyl_tRNA"
+      "lbl" : "cysteine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001112",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000698",
       "meta" : {
         "definition" : {
-          "val" : "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.",
-          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+          "val" : "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "antiparallel beta strand",
+          "val" : "gene with stop codon redefined as pyrrolysine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:0000341"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Range."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "antiparallel_beta_strand"
+      "lbl" : "gene_with_stop_codon_redefined_as_pyrrolysine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000260",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001545",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.",
+          "val" : "A sequence variant that changes polyadenylation with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "glutamyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "glutamyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "glutamyl-transfer RNA",
+          "val" : "polyadenylation variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:49:40Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "glutamyl_tRNA"
+      "lbl" : "polyadenylation_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001591",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000214",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.",
+          "val" : "A primary transcript encoding aspartyl tRNA (SO:0000257).",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "frame restoring variant",
+          "val" : "aspartic acid tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:41:09Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "frame_restoring_variant"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym",
-      "type" : "PROPERTY",
-      "lbl" : "has_exact_synonym"
+      "lbl" : "aspartic_acid_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001590",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000693",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby at least one of the bases in the terminator codon is changed.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that encodes an mRNA that is recoded.",
+          "xrefs" : [ "SO:xp" ]
         },
-        "xrefs" : [ {
-          "val" : "http://vat.gersteinlab.org/formats.php"
-        }, {
-          "val" : "loinc:LA6700-2"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "terminal_codon_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "terminator codon variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "terminal codon variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAT:endOverlap",
+          "val" : "gene with recoded mRNA",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001625"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "The terminal codon may be the terminator, or in an incomplete transcript the last available codon."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:40:37Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "terminator_codon_variant"
+      "lbl" : "gene_with_recoded_mRNA"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001593",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001540",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which alters the level of a transcript.",
+          "xrefs" : [ "SO:ke" ]
+        },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "minus 2 frameshift variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "-2 frameshift variant",
+          "val" : "level of transcript variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:47:07Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:41:52Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_2_frameshift_variant"
+      "lbl" : "level_of_transcript_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000262",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000692",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that encodes a dicistronic transcript.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "histidyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "histidyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "histidyl-transfer RNA",
+          "val" : "gene with dicistronic transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60408,203 +64455,209 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "histidyl_tRNA"
+      "lbl" : "gene_with_dicistronic_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000261",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001542",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.",
+          "val" : "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "glycyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "glycyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "glycyl-transfer RNA",
+          "val" : "increased transcript level variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:48:17Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "glycyl_tRNA"
+      "lbl" : "increased_transcript_level_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001592",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000211",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.",
-          "xrefs" : [ "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535" ]
+          "val" : "A primary transcript encoding alanyl tRNA.",
+          "xrefs" : [ "SO:ke" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "minus 1 frameshift variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "-1 frameshift variant",
+          "val" : "alanine tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:41:30Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "minus_1_frameshift_variant"
+      "lbl" : "alanine_tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#recombined_to",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000695",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence used in experiment.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Requested by Lynn Crosby, jan 2006." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T02:20:07Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "recombined_to"
+      "type" : "CLASS",
+      "lbl" : "reagent"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001108",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000694",
       "meta" : {
         "definition" : {
-          "val" : "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins.",
-          "xrefs" : [ "EBIBS:GAR", "Http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater.",
+          "xrefs" : [ "SO:cb" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta bulge loop",
+          "val" : "single nucleotide polymorphism",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00209"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_bulge_loop"
+      "lbl" : "SNP"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001107",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001541",
       "meta" : {
         "definition" : {
-          "val" : "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/Beta_bulge"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta bulge",
+          "val" : "decreased transcript level",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:47:47Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00208"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_bulge"
+      "lbl" : "decreased_transcript_level_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001109",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000210",
       "meta" : {
         "definition" : {
-          "val" : "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3.",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A primary transcript encoding a transfer RNA (SO:0000253).",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "beta bulge loop five",
+          "val" : "tRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00210"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "beta_bulge_loop_five"
+      "lbl" : "tRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001104",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000691",
       "meta" : {
         "definition" : {
-          "val" : "Amino acid involved in the activity of an enzyme.",
-          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+          "val" : "The initiator methionine that has been cleaved from a mature polypeptide sequence.",
+          "xrefs" : [ "EBIBS:GAR" ]
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "act_site",
-          "xrefs" : [ "uniprot:feature_type" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "active site residue",
+          "val" : "initiator methionine",
           "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "init_met",
+          "xrefs" : [ "uniprot:feature_type" ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "catalytic residue",
+          "val" : "cleaved initiator methionine",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Discrete."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00026"
+          "val" : "BS:00067"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "catalytic_residue"
+      "lbl" : "cleaved_initiator_methionine"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000257",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000690",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A gene that encodes a polycistronic transcript.",
+          "xrefs" : [ "SO:xp" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "aspartyl tRNA",
+          "val" : "gene with polycistronic transcript",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_with_polycistronic_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00203",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0000912"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000209",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding a ribosomal RNA.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "aspartyl-transfer ribonucleic acid",
+          "val" : "ribosomal RNA primary transcript",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "aspartyl-transfer RNA",
+          "val" : "rRNA primary transcript",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60613,135 +64666,142 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "aspartyl_tRNA"
+      "lbl" : "rRNA_primary_transcript"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001587",
+      "id" : "http://purl.obolibrary.org/obo/BS_00202",
       "meta" : {
-        "definition" : {
-          "val" : "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide.",
-          "xrefs" : [ "SO:ke" ]
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001106"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001537",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that changes one or more structural features.",
+          "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "loinc:LA6699-8"
-        }, {
           "val" : "http://vat.gersteinlab.org/formats.php"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "nonsense",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:STOP_GAINED",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "nonsense codon",
+          "pred" : "hasRelatedSynonym",
+          "val" : "structural variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAT:prematureStop",
-          "xrefs" : [ ]
+          "val" : "Jannovar:structural_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "stop gained",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "VAT:svOverlap",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:stop_gained",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:31:01Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "structural_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000206",
+      "meta" : {
+        "definition" : {
+          "val" : "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:stop_gained",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "stop codon gained",
+          "val" : "Short interspersed element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:stopgain",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:stop_gained",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:stop-gained-near-splice",
+          "val" : "Short interspersed nuclear element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:stop-gained",
+          "val" : "SINE element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:37:52Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence)."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stop_gained"
+      "lbl" : "SINE_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001103",
+      "id" : "http://purl.obolibrary.org/obo/BS_00207",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001132"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001536",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions.",
-          "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
+          "val" : "A variant whereby the effect is evaluated with respect to a reference.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "comments" : [ "Updated after request from Lea Starita, lea.starita@gmail.com from the NCBI." ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide zinc ion contact site",
+          "val" : "functional variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Zn_contact_site",
+          "val" : "functional effect variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00185"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:30:25Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_zinc_ion_contact_site"
+      "lbl" : "functional_effect_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000256",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000689",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.",
+          "val" : "A match against cDNA sequence.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "asparaginyl tRNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "asparaginyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "asparaginyl-transfer ribonucleic acid",
+          "val" : "cDNA match",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60750,25 +64810,29 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "asparaginyl_tRNA"
+      "lbl" : "cDNA_match"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000259",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000205",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Three_prime_untranslated_region"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "glutaminyl tRNA",
+          "val" : "INSDC_feature:3'UTR",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "glutaminyl-transfer ribonucleic acid",
+          "val" : "three prime untranslated region",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "glutaminyl-transfer RNA",
+          "val" : "three prime UTR",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60777,162 +64841,127 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "glutaminyl_tRNA"
+      "lbl" : "three_prime_UTR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001106",
+      "id" : "http://purl.obolibrary.org/obo/BS_00206",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001129"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000208",
       "meta" : {
         "definition" : {
-          "val" : "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4).",
-          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+          "val" : "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long.",
+          "xrefs" : [ "http://www.genetics.org/cgi/reprint/156/4/1983.pdf" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "asx motif",
+          "val" : "TIR element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "terminal inverted repeat element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00202"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "asx_motif"
+      "lbl" : "terminal_inverted_repeat_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001589",
+      "id" : "http://purl.obolibrary.org/obo/BS_00205",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001131"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001539",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three.",
+          "val" : "A sequence variant that affects the functioning of a translational product with respect to a reference sequence.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://vat.gersteinlab.org/formats.php"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "loinc:LA6694-9"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasNarrowSynonym",
-          "val" : "VAT:insertionFS",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "frameshift_coding",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:frameshift_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "frameshift_",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:FRAME_SHIFT",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:frameshift_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:frameshift",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:frameshift block substitution",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:frameshift substitution",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "frameshift variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:frameshift-near-splice",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasNarrowSynonym",
-          "val" : "VAT:deletionFS",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:frameshift_variant",
+          "val" : "translational product variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term:Frameshift variations - In coding sequence, resulting in a frameshift."
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:40:19Z"
+          "val" : "2010-03-22T11:46:15Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "frameshift_variant"
+      "lbl" : "translational_product_function_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001105",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001538",
       "meta" : {
         "definition" : {
-          "val" : "Residues which interact with a ligand.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A sequence variant which alters the functioning of a transcript with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide ligand contact",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "protein-ligand interaction",
+          "val" : "transcript function variant",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00157"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:32:58Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_ligand_contact"
+      "lbl" : "transcript_function_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000258",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000207",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region.",
+          "val" : "SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Simple_sequence_length_polymorphism"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "cysteinyl-transfer ribonucleic acid",
+          "val" : "simple sequence length variation",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "cysteinyl-transfer RNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "simple sequence length polymorphism",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "cysteinyl tRNA",
+          "pred" : "hasRelatedSynonym",
+          "val" : "SSLP",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -60941,98 +64970,113 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "cysteinyl_tRNA"
+      "lbl" : "simple_sequence_length_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000253",
+      "id" : "http://purl.obolibrary.org/obo/BS_00204",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001130"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000686",
       "meta" : {
         "definition" : {
-          "val" : "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.",
-          "xrefs" : [ "ISBN:0198506732", "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005" ]
+          "val" : "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/TRNA"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:tRNA",
+          "val" : "translocation element",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "translocation_element"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001533",
+      "meta" : {
+        "definition" : {
+          "val" : "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_qualifier:unknown",
+          "val" : "cryptic splice signal",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "transfer ribonucleic acid",
+          "pred" : "hasExactSynonym",
+          "val" : "cryptic splice site",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This term is mapped to MGED. Do not obsolete without consulting MGED ontology."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-11T03:25:06Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "tRNA"
+      "lbl" : "cryptic_splice_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001100",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000202",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.",
-          "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
+          "val" : "The coding exon that is most 3-prime on a given transcript.",
+          "xrefs" : [ "SO:ma" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide molybdenum ion contact site",
+          "val" : "three prime coding exon",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Mo_contact_site",
+          "pred" : "hasRelatedSynonym",
+          "val" : "3' coding exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00141"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_molybdenum_ion_contact_site"
+      "lbl" : "three_prime_coding_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000252",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000685",
       "meta" : {
         "definition" : {
-          "val" : "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.",
-          "xrefs" : [ "ISBN:0198506732", "http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html" ]
+          "val" : "DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I.",
+          "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
-        "xrefs" : [ {
-          "val" : "http://en.wikipedia.org/wiki/RRNA"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasBroadSynonym",
-          "val" : "INSDC_qualifier:unknown",
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_qualifier:DNase_I_hypersensitive_site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "ribosomal ribonucleic acid",
+          "val" : "DNaseI hypersensitive site",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ribosomal RNA",
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_feature:regulatory",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "INSDC_feature:rRNA",
+          "val" : "DHS",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -61041,165 +65085,100 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA"
+      "lbl" : "DNaseI_hypersensitive_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001583",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001532",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.",
-          "xrefs" : [ "EBI:fc", "EBI:gr", "SO:ke" ]
+          "val" : "A region recognized by a recombinase.",
+          "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://en.wikipedia.org/wiki/Missense_mutation"
-        }, {
-          "val" : "loinc:LA6698-0"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        }, {
-          "val" : "http://vat.gersteinlab.org/formats.php"
-        }, {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+          "val" : "http://en.wikipedia.org/wiki/Recombination_Signal_Sequences"
         } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:NON_SYNONYMOUS_CODING",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:missense_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "ANNOVAR:nonsynonymous SNV",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "VAAST:non_synonymous_codon",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAT:nonsynonymous",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:missense_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:missense",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "missense codon",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "missense",
-          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:missense_variant",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:missense-near-splice",
+          "val" : "recombination signal sequence",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001584"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:35:49Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001783"
+          "val" : "2010-03-11T03:16:47Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution."
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "missense_variant"
+      "lbl" : "recombination_signal_sequence"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001102",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000201",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.",
-          "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
+          "val" : "An exon that is bounded by 5' and 3' splice sites.",
+          "xrefs" : [ "PMID:10373547" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "polypeptide tungsten ion contact site",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "W_contact_site",
+          "val" : "interior exon",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00143"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_tungsten_ion_contact_site"
+      "lbl" : "interior_exon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001586",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000204",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.",
+          "xrefs" : [ "http://www.insdc.org/files/feature_table.html" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+          "val" : "http://en.wikipedia.org/wiki/5'_UTR"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "non conservative missense codon",
+          "val" : "INSDC_feature:5'UTR",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "non conservative missense variant",
+          "val" : "5' UTR",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:37:16Z"
+          "pred" : "hasExactSynonym",
+          "val" : "five_prime_untranslated_region",
+          "xrefs" : [ ]
         }, {
+          "pred" : "hasExactSynonym",
+          "val" : "five prime UTR",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "non_conservative_missense_variant"
+      "lbl" : "five_prime_UTR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000255",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000688",
       "meta" : {
         "definition" : {
-          "val" : "A primary transcript encoding a small ribosomal subunit RNA.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence.",
+          "xrefs" : [ "SO:ls" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "rRNA small subunit primary transcript",
+          "val" : "golden path",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -61208,65 +65187,73 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "rRNA_small_subunit_primary_transcript"
+      "lbl" : "golden_path"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001585",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001535",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A P-element is a DNA transposon responsible for hybrid dysgenesis. P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain.",
+          "xrefs" : [ "PMID:6309410", "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        } ],
+        "comments" : [ "Moved from under DNA_transposon (SO:0000182) by Dave Sant as per request from GitHub issue #488 on June 25, 2020" ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "neutral missense codon",
+          "pred" : "hasExactSynonym",
+          "val" : "DTP transposon",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "quiet missense codon",
+          "pred" : "hasExactSynonym",
+          "val" : "P TIR transposon",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conservative missense codon",
+          "val" : "P-element",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "conservative missense variant",
+          "val" : "P element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "P transposable element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
-          "val" : "kareneilbeck"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:36:40Z"
+          "val" : "2010-03-12T03:40:33Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "conservative_missense_variant"
+      "lbl" : "P_TIR_transposon"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000254",
+      "id" : "http://purl.obolibrary.org/obo/BS_00209",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001108"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000203",
       "meta" : {
         "definition" : {
-          "val" : "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.",
+          "val" : "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated.",
           "xrefs" : [ "SO:ke" ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "alanyl-transfer ribonucleic acid",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "alanyl-transfer RNA",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "alanyl tRNA",
+          "val" : "untranslated region",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -61275,90 +65262,162 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "alanyl_tRNA"
+      "lbl" : "UTR"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001101",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001534",
       "meta" : {
         "definition" : {
-          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.",
-          "xrefs" : [ "EBIBS:GAR" ]
+          "val" : "A polypeptide region that targets a polypeptide to the nuclear rim.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "PMID:16027110"
+        } ],
         "synonyms" : [ {
-          "pred" : "hasExactSynonym",
-          "val" : "polypeptide nickel ion contact site",
+          "pred" : "hasRelatedSynonym",
+          "val" : "nuclear rim localization signal",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-11T03:31:30Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "nuclear_rim_localization_signal"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BS_00208",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
         }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001107"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000687",
+      "meta" : {
+        "definition" : {
+          "val" : "The space between two bases in a sequence which marks the position where a deletion has occurred.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Ni_contact_site",
+          "val" : "deletion junction",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "BS:00142"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polypeptide_nickel_ion_contact_site"
+      "lbl" : "deletion_junction"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001580",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001573",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the coding sequence.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
         },
         "xrefs" : [ {
           "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "VAAST:coding_sequence_variant",
+          "val" : "intron gain",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "coding variant",
+          "val" : "intron gain variant",
           "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         }, {
-          "pred" : "hasExactSynonym",
-          "val" : "coding sequence variant",
-          "xrefs" : [ ]
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:31:25Z"
         }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "intron_gain_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000242",
+      "meta" : {
+        "definition" : {
+          "val" : "The untranslated sequence separating the 'cistrons' of multicistronic mRNA.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:CDS",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "snpEff:CODON_CHANGE",
+          "val" : "untranslated region polycistronic mRNA",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "untranslated_region_polycistronic_mRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000241",
+      "meta" : {
+        "definition" : {
+          "val" : "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal.",
+          "xrefs" : [ "SO:cjm" ]
+        },
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "codon variant",
+          "val" : "internal UTR",
           "xrefs" : [ ]
-        }, {
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "internal_UTR"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001572",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant whereby an exon is lost from the transcript.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
+        "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:coding",
-          "xrefs" : [ ]
+          "val" : "snpEff:EXON_DELETED",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "codon_variant",
-          "xrefs" : [ ]
+          "val" : "Jannovar:exon_loss_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VEP:coding_sequence_variant",
+          "val" : "exon loss",
           "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:coding_sequence_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
         } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
@@ -61368,279 +65427,290 @@
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:34:36Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
-          "val" : "SO:0001581"
+          "val" : "2010-03-22T02:31:09Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "coding_sequence_variant"
+      "lbl" : "exon_loss_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001582",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001575",
       "meta" : {
         "definition" : {
-          "val" : "A codon variant that changes at least one base of the first codon of a transcript.",
+          "val" : "A splice variant that changes the 2 base pair region at the 5' end of an intron.",
           "xrefs" : [ "SO:ke" ]
         },
         "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
         }, {
-          "val" : "http://vat.gersteinlab.org/formats.php"
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         }, {
-          "val" : "loinc:LA6695-6"
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:initiator_codon_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
+          "val" : "Jannovar:splice_donor_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "initiator codon change",
-          "xrefs" : [ ]
+          "val" : "VEP:splice_donor_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "VAT:startOverlap",
+          "val" : "splice donor variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "initiatior codon variant",
-          "xrefs" : [ ]
+          "val" : "snpEff:SPLICE_SITE_DONOR",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "snpEff:NON_SYNONYMOUS_START",
-          "xrefs" : [ ]
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:splice_donor_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:splice-donor",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called."
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:32:10Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:35:18Z"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "initiator_codon_variant"
+      "lbl" : "splice_donor_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000251",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000244",
       "meta" : {
         "synonyms" : [ {
           "pred" : "hasRelatedSynonym",
-          "val" : "eight-cutter_restriction_site",
+          "val" : "4-cutter_restriction_site",
           "xrefs" : [ ]
         }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "8-cutter_restriction_site",
+          "val" : "four-cutter_restriction_sit",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
-      "lbl" : "eight_cutter_restriction_site"
+      "lbl" : "four_cutter_restriction_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/so#processed_from",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001574",
       "meta" : {
         "definition" : {
-          "val" : "Inverse of processed_into.",
-          "xrefs" : [ "http://precedings.nature.com/documents/3495/version/1" ]
+          "val" : "A splice variant that changes the 2 base region at the 3' end of an intron.",
+          "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        }, {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:SPLICE_SITE_ACCEPTOR",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:splice_acceptor_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:splice_acceptor_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:splice-acceptor",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splice acceptor variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:splice_acceptor_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2009-08-19T12:14:00Z"
+          "val" : "2010-03-22T02:31:52Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "Example: miRNA processed_from miRNA_primary_transcript."
         } ]
       },
-      "type" : "PROPERTY",
-      "lbl" : "processed_from"
+      "type" : "CLASS",
+      "lbl" : "splice_acceptor_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000250",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000243",
       "meta" : {
         "definition" : {
-          "val" : "A post_transcriptionally modified base.",
+          "val" : "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation.",
           "xrefs" : [ "SO:ke" ]
         },
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Internal_ribosome_entry_site"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "modified RNA base feature",
+          "val" : "internal ribosomal entry sequence",
           "xrefs" : [ ]
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        } ]
-      },
-      "type" : "CLASS",
-      "lbl" : "modified_RNA_base_feature"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000249",
-      "meta" : {
-        "synonyms" : [ {
+        }, {
           "pred" : "hasRelatedSynonym",
-          "val" : "6-cutter_restriction_site",
+          "val" : "internal ribosome entry sequence",
           "xrefs" : [ ]
         }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "six-cutter_restriction_site",
+          "pred" : "hasExactSynonym",
+          "val" : "internal ribosome entry site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "internal ribosomal entry site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "IRES",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "six_cutter_restriction_site"
+      "lbl" : "internal_ribosome_entry_site"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001577",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001571",
       "meta" : {
         "definition" : {
-          "val" : "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "A sequence variant whereby a new splice site is created due to the activation of a new donor.",
+          "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
-        } ],
         "synonyms" : [ {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:codingComplex-near-splice",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "complex_indel",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:codingComplex",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "complex transcript variant",
-          "xrefs" : [ ]
-        }, {
           "pred" : "hasExactSynonym",
-          "val" : "complex change in transcript",
+          "val" : "cryptic splice donor",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border."
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:33:03Z"
+          "val" : "2010-03-22T02:30:35Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "complex_transcript_variant"
+      "lbl" : "cryptic_splice_donor"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000246",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000240",
       "meta" : {
         "definition" : {
-          "val" : "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A deviation in chromosome structure or number.",
+          "xrefs" : [ ]
         },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "chromosome variation",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "polyadenylated"
+      "lbl" : "chromosome_variation"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001576",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001570",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant that changes the structure of the transcript.",
+          "val" : "A sequence variant whereby a new splice site is created due to the activation of a new acceptor.",
           "xrefs" : [ "SO:ke" ]
         },
-        "xrefs" : [ {
-          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
-        }, {
-          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:transcript_variant",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "Jannovar:transcript_variant",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "snpEff:TRANSCRIPT",
+          "val" : "cryptic splice acceptor",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-22T02:32:41Z"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "sequence"
+          "val" : "2010-03-22T02:30:11Z"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_variant"
+      "lbl" : "cryptic_splice_acceptor"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000245",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000239",
       "meta" : {
+        "definition" : {
+          "val" : "The sequences extending on either side of a specific region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "flanking region",
+          "xrefs" : [ ]
+        } ],
         "basicPropertyValues" : [ {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_by_polyadenylation_status"
+      "lbl" : "flanking_region"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000248",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000238",
       "meta" : {
         "definition" : {
-          "val" : "A kind of kind of sequence alteration where the copies of a region present varies across a population.",
-          "xrefs" : [ "SO:ke" ]
+          "val" : "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats.",
+          "xrefs" : [ "http://www.genetics.org/cgi/reprint/156/4/1983.pdf" ]
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "sequence length alteration",
+          "val" : "foldback element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "long inverted repeat element",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "LVR element",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
@@ -61649,492 +65719,8907 @@
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "sequence_length_alteration"
+      "lbl" : "foldback_element"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001579",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001569",
       "meta" : {
+        "definition" : {
+          "val" : "A sequence variant causing a new (functional) splice site.",
+          "xrefs" : [ "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html" ]
+        },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "transcript sequence variant",
+          "val" : "cryptic splice site activation",
           "xrefs" : [ ]
         } ],
         "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:29:41Z"
+        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "transcript_sequence_variant"
+      "lbl" : "cryptic_splice_site_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0001578",
+      "id" : "http://purl.obolibrary.org/obo/SO_0001566",
       "meta" : {
         "definition" : {
-          "val" : "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript.",
+          "val" : "A sequence variant located within a regulatory region.",
           "xrefs" : [ "SO:ke" ]
         },
+        "comments" : [ "EBI term: Regulatory region variations - In regulatory region annotated by Ensembl." ],
         "xrefs" : [ {
           "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
-        }, {
-          "val" : "http://vat.gersteinlab.org/formats.php"
-        }, {
-          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
         }, {
           "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Seattleseq:stop-lost",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VEP:stop_lost",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "ANNOVAR:stoploss",
-          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAT:removedStop",
-          "xrefs" : [ ]
-        }, {
-          "pred" : "hasExactSynonym",
-          "val" : "VAAST:stop_lost",
+          "val" : "regulatory region variant",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Jannovar:stop_lost",
-          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ]
-        }, {
-          "pred" : "hasRelatedSynonym",
-          "val" : "Seattleseq:stop-lost-near-splice",
-          "xrefs" : [ ]
+          "val" : "regulatory_region_",
+          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#ebi_variants"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "stop codon lost",
-          "xrefs" : [ ]
+          "val" : "VEP:regulatory_region_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "snpEff:STOP_LOST",
-          "xrefs" : [ ]
+          "val" : "snpEff:REGULATION",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "stop lost",
-          "xrefs" : [ "http://ensembl.org/info/docs/variation/index.html" ]
+          "val" : "Jannovar:regulatory_region_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
-          "val" : "2010-03-23T03:46:42Z"
-        }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         }, {
-          "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
-          "val" : "EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon."
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:28:48Z"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
           "val" : "kareneilbeck"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "stop_lost"
+      "lbl" : "regulatory_region_variant"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/SO_0000247",
+      "id" : "http://purl.obolibrary.org/obo/SO_0000235",
       "meta" : {
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+        "definition" : {
+          "val" : "A DNA site where a transcription factor binds.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "TF binding site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "transcription factor binding site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "sequence"
         } ]
       },
       "type" : "CLASS",
-      "lbl" : "mRNA_not_polyadenylated"
-    } ],
-    "edges" : [ {
-      "sub" : "http://purl.obolibrary.org/obo/SO_0001905",
-      "pred" : "http://purl.obolibrary.org/obo/so#derives_from",
-      "obj" : "http://purl.obolibrary.org/obo/SO_0001799"
+      "lbl" : "TF_binding_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000234",
+      "meta" : {
+        "definition" : {
+          "val" : "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.",
+          "xrefs" : [ "SO:ma" ]
+        },
+        "comments" : [ "An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://www.gencodegenes.org/gencode_biotypes.html"
+        }, {
+          "val" : "http://en.wikipedia.org/wiki/MRNA"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "messenger RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:mRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "protein_coding_transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "mRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001565",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant whereby a two genes have become joined.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "gene fusion",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:28:28Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_fusion"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000237",
+      "meta" : {
+        "definition" : {
+          "val" : "An attribute describing a transcript.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transcript attribute",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "transcript_attribute"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001568",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that changes the process of splicing.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:splicing_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "splicing variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:29:22Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "splicing_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001567",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:stop_retained",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:NON_SYNONYMOUS_STOP",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:stop_retained_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "stop retained variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:stop_retained_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:stop_retained_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:SYNONYMOUS_STOP",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-04-19T05:02:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "stop_retained_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000236",
+      "meta" : {
+        "definition" : {
+          "val" : "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER.",
+          "xrefs" : [ "SGD:rb", "SO:ma" ]
+        },
+        "comments" : [ "The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "open reading frame",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "ORF"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001562",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide post translational processing variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:59:06Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "polypeptide_post_translational_processing_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000231",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding a small nuclear RNA (SO:0000274).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "snRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "snRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001561",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide partial loss of function",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:58:32Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "polypeptide_partial_loss_of_function"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000230",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding valyl tRNA (SO:000273).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "valine tRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "valine_tRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#partial_evidence_for_feature",
+      "meta" : {
+        "definition" : {
+          "val" : "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "partial_evidence_for_feature"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001564",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant where the structure of the gene is changed.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:gene_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:GENE",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "gene structure variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:gene_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:28:01Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "gene_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000233",
+      "meta" : {
+        "definition" : {
+          "val" : "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "A processed transcript cannot contain introns." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Mature_transcript"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "mature transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "mature_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000232",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520)." ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "snoRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "snoRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001563",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant where copies of a feature (CNV) are either increased or decreased.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "copy number change",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:27:33Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "copy_number_change"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001560",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "inactive ligand binding site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:58:00Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "inactive_ligand_binding_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000228",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding tryptophanyl tRNA (SO:000271).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "tryptophan tRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "tryptophan_tRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001559",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide loss of function variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:56:58Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "polypeptide_loss_of_function_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001558",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide localization variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:56:37Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "polypeptide_localization_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000227",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding threonyl tRNA (SO:000270).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "threonine tRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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+      "lbl" : "threonine_tRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/so#trans_spliced_to",
+      "meta" : {
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+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
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+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "PROPERTY",
+      "lbl" : "trans_spliced_to"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000229",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding tyrosyl tRNA (SO:000272).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "tyrosine tRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "tyrosine_tRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001555",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which decreases the translational product level with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "decrease translational product level",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
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+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:54:25Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "decreased_translational_product_level"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000224",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding phenylalanyl tRNA (SO:0000267).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "phenylalanine tRNA primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
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+          "val" : "sequence"
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+      },
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+      "lbl" : "phenylalanine_tRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001554",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which changes polypeptide functioning with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide function variant",
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+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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+          "val" : "2010-03-22T11:53:54Z"
+        } ]
+      },
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+      "lbl" : "polypeptide_function_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000223",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding methionyl tRNA (SO:0000266).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "methionine tRNA primary transcript",
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+        "basicPropertyValues" : [ {
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+      "lbl" : "methionine_tRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001557",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which causes gain of polypeptide function with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
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+          "val" : "polypeptide gain of function variant",
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+      },
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+      "lbl" : "polypeptide_gain_of_function_variant"
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+      "meta" : {
+        "definition" : {
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+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
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+          "val" : "serine tRNA primary transcript",
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+        "basicPropertyValues" : [ {
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+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding prolyl tRNA (SO:0000268).",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
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+          "val" : "proline tRNA primary transcript",
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+      "lbl" : "proline_tRNA_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001556",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which increases the translational product level with respect to a reference sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "increase translational product level",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T11:55:25Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "increased_translational_product_level"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001595",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which causes a disruption of the translational reading frame, by shifting two bases backward.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "+2 frameshift variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "plus 2 frameshift variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:42:23Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "plus_2_frameshift_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001111",
+      "meta" : {
+        "definition" : {
+          "val" : "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array.",
+          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+        },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Beta_sheet"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "strand",
+          "xrefs" : [ "uniprot:feature_type" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#BS"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00042"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "beta_strand"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000264",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "leucyl tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "leucyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "leucyl-transfer RNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "leucyl_tRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001594",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward.",
+          "xrefs" : [ "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "+1 frameshift variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "plus 1 frameshift variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:42:06Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "plus_1_frameshift_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001110",
+      "meta" : {
+        "definition" : {
+          "val" : "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4.",
+          "xrefs" : [ "EBIBS:GAR", "http://www.ebi.ac.uk/msd-srv/msdmotif/" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "beta bulge loop six",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00211"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "beta_bulge_loop_six"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000263",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "isoleucyl tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "isoleucyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "isoleucyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "isoleucyl_tRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001597",
+      "meta" : {
+        "definition" : {
+          "val" : "A secondary structure variant that compensate for the change made by a previous variant.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "compensatory transcript secondary structure variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:43:54Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "compensatory_transcript_secondary_structure_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001113",
+      "meta" : {
+        "definition" : {
+          "val" : "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets.",
+          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+        },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "parallel beta strand",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00151"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "parallel_beta_strand"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000266",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "methionyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "methionyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "methionyl tRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "methionyl_tRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000265",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "lysyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "lysyl tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "lysyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "lysyl_tRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001112",
+      "meta" : {
+        "definition" : {
+          "val" : "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets.",
+          "xrefs" : [ "EBIBS:GAR", "UniProt:curation_manual" ]
+        },
+        "comments" : [ "Range." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "antiparallel beta strand",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:0000341"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "antiparallel_beta_strand"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001596",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant within a transcript that changes the secondary structure of the RNA product.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "transcript secondary structure variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:43:18Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "transcript_secondary_structure_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001591",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "frame restoring variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:41:09Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "frame_restoring_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000260",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "glutamyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "glutamyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "glutamyl tRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "glutamyl_tRNA"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym",
+      "type" : "PROPERTY",
+      "lbl" : "has_exact_synonym"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001590",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant whereby at least one of the bases in the terminator codon is changed.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "The terminal codon may be the terminator, or in an incomplete transcript the last available codon." ],
+        "xrefs" : [ {
+          "val" : "loinc:LA6700-2"
+        }, {
+          "val" : "http://vat.gersteinlab.org/formats.php"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "terminal codon variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAT:endOverlap",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "terminator codon variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "terminal_codon_variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001625"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:40:37Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "terminator_codon_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001593",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which causes a disruption of the translational reading frame, by shifting two bases forward.",
+          "xrefs" : [ ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "-2 frameshift variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "minus 2 frameshift variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:41:52Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "minus_2_frameshift_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000262",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "histidyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "histidyl tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "histidyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "histidyl_tRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001592",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead.",
+          "xrefs" : [ "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "-1 frameshift variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "minus 1 frameshift variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:41:30Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "minus_1_frameshift_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000261",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "glycyl-transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "glycyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "glycyl tRNA",
+          "xrefs" : [ ]
+        } ],
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+      "type" : "CLASS",
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+        "synonyms" : [ {
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+          "val" : "BS:00209"
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+      "type" : "CLASS"
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+          "val" : "aspartyl-transfer RNA",
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+          "val" : "aspartyl-transfer ribonucleic acid",
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+          "val" : "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region.",
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+        },
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+          "val" : "VAAST:stop_gained",
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+      "meta" : {
+        "definition" : {
+          "val" : "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position.",
+          "xrefs" : [ "ISBN:0198506732", "http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005" ]
+        },
+        "comments" : [ "This term is mapped to MGED. Do not obsolete without consulting MGED ontology." ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/TRNA"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "transfer RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "transfer ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_qualifier:unknown",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "tRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001100",
+      "meta" : {
+        "definition" : {
+          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions.",
+          "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "Mo_contact_site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide molybdenum ion contact site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00141"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "polypeptide_molybdenum_ion_contact_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001584",
+      "meta" : {
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
+          "val" : "http://purl.obolibrary.org/obo/SO_0001583"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
+        } ],
+        "deprecated" : true
+      },
+      "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000252",
+      "meta" : {
+        "definition" : {
+          "val" : "rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.",
+          "xrefs" : [ "ISBN:0198506732", "http://www.insdc.org/files/feature_table.html" ]
+        },
+        "comments" : [ "Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493" ],
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#SOFA" ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/RRNA"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasBroadSynonym",
+          "val" : "INSDC_qualifier:unknown",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ribosomal RNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "ribosomal ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "INSDC_feature:rRNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "rRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001583",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.",
+          "xrefs" : [ "EBI:fc", "EBI:gr", "SO:ke" ]
+        },
+        "comments" : [ "EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution." ],
+        "xrefs" : [ {
+          "val" : "http://en.wikipedia.org/wiki/Missense_mutation"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
+        }, {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http://vat.gersteinlab.org/formats.php"
+        }, {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        }, {
+          "val" : "loinc:LA6698-0"
+        }, {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "VAAST:non_synonymous_codon",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "missense",
+          "xrefs" : [ "ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd" ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "ANNOVAR:nonsynonymous SNV",
+          "xrefs" : [ "http://www.openbioinformatics.org/annovar/annovar_download.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:missense_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:missense_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:missense_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:missense",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "missense codon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "Seattleseq:missense-near-splice",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:NON_SYNONYMOUS_CODING",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAT:nonsynonymous",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001584"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001783"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:35:49Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "missense_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001102",
+      "meta" : {
+        "definition" : {
+          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions.",
+          "xrefs" : [ "EBIBS:GAR", "SO:cb" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide tungsten ion contact site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "W_contact_site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00143"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "polypeptide_tungsten_ion_contact_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000255",
+      "meta" : {
+        "definition" : {
+          "val" : "A primary transcript encoding a small ribosomal subunit RNA.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "rRNA small subunit primary transcript",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "rRNA_small_subunit_primary_transcript"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001586",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "non conservative missense codon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "non conservative missense variant",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
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+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:37:16Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "non_conservative_missense_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001585",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        } ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "conservative missense variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "quiet missense codon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "conservative missense codon",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "neutral missense codon",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:36:40Z"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "conservative_missense_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001101",
+      "meta" : {
+        "definition" : {
+          "val" : "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions.",
+          "xrefs" : [ "EBIBS:GAR" ]
+        },
+        "subsets" : [ "http://purl.obolibrary.org/obo/so#biosapiens" ],
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "polypeptide nickel ion contact site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Ni_contact_site",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "BS:00142"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "polypeptide_nickel_ion_contact_site"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000254",
+      "meta" : {
+        "definition" : {
+          "val" : "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "alanyl tRNA",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "alanyl-transfer ribonucleic acid",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "alanyl-transfer RNA",
+          "xrefs" : [ ]
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "alanyl_tRNA"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001580",
+      "meta" : {
+        "definition" : {
+          "val" : "A sequence variant that changes the coding sequence.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "xrefs" : [ {
+          "val" : "http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp"
+        }, {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        }, {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences"
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+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "VEP:coding_sequence_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:coding_sequence_variant",
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+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "coding variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "codon variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "snpEff:CODON_CHANGE",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
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+          "pred" : "hasExactSynonym",
+          "val" : "snpEff:CDS",
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+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "codon_variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAAST:coding_sequence_variant",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "coding sequence variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Seattleseq:coding",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
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+        "basicPropertyValues" : [ {
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+          "val" : "kareneilbeck"
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+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId",
+          "val" : "SO:0001581"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
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+          "val" : "2010-03-22T02:34:36Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "coding_sequence_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0001582",
+      "meta" : {
+        "definition" : {
+          "val" : "A codon variant that changes at least one base of the first codon of a transcript.",
+          "xrefs" : [ "SO:ke" ]
+        },
+        "comments" : [ "This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called." ],
+        "xrefs" : [ {
+          "val" : "http://snpeff.sourceforge.net/SnpEff_manual.html"
+        }, {
+          "val" : "EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html"
+        }, {
+          "val" : "http://vat.gersteinlab.org/formats.php"
+        }, {
+          "val" : "loinc:LA6695-6"
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+        "synonyms" : [ {
+          "pred" : "hasExactSynonym",
+          "val" : "initiatior codon variant",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "Jannovar:initiator_codon_variant",
+          "xrefs" : [ "http://doc-openbio.readthedocs.org/projects/jannovar/en/master/var_effects.html" ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "initiator codon change",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasExactSynonym",
+          "val" : "VAT:startOverlap",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "snpEff:NON_SYNONYMOUS_START",
+          "xrefs" : [ ],
+          "synonymType" : "http://purl.obolibrary.org/obo/so#VAR"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "sequence"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by",
+          "val" : "kareneilbeck"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
+          "val" : "2010-03-22T02:35:18Z"
+        } ]
+      },
+      "type" : "CLASS",
+      "lbl" : "initiator_codon_variant"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/SO_0000251",
+      "meta" : {
+        "synonyms" : [ {
+          "pred" : "hasRelatedSynonym",
+          "val" : "8-cutter_restriction_site",
+          "xrefs" : [ ]
+        }, {
+          "pred" : "hasRelatedSynonym",
+          "val" : "eight-cutter_restriction_site",
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-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000992",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000914" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#derives_from",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000153"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000280",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000704" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000995",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000234" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000993"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000079",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000673" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000879"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000634",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000234" ],
@@ -74784,20 +82413,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#part_of",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000980"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000078",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000673" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000880"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0001870",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000655" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#transcribed_from",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000165"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000633",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000234" ],
@@ -74805,13 +82420,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000878"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_1001197",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000185" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000879"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_1001264",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000234" ],
@@ -74826,13 +82434,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#transcribed_to",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000078"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000166",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000165" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000277"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000722",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000692" ],
@@ -74840,13 +82441,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#transcribed_to",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000716"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000121",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000112" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0001030"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_1000145",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_1000045" ],
@@ -74854,13 +82448,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0001516"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0001012",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000696" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0001185"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0001033",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000745" ],
@@ -74892,13 +82479,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#part_of",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000101"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000795",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000815" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000814"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0001476",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000155" ],
@@ -74906,20 +82486,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000782"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000588",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000188" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0001186"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000451",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0001217" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#transcribed_to",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000871"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000287",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000704" ],
@@ -74941,16 +82507,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_part",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000104"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000872",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000234" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#adjacent_to",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000636"
-      }, {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000870"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000666",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000188" ],
@@ -74965,13 +82521,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0001462",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0001085" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_part",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000149"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000281",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000280" ],
@@ -74982,20 +82531,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000784"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000380",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000715" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0001186"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0005858",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000330" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000860"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000283",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000111" ],
@@ -75013,20 +82548,6 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000782"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_1000030",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_1000028" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_part",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_1000036"
-      } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000637",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000155" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783"
-      } ]
     }, {
       "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000329",
       "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000108" ],
@@ -75034,15 +82555,8 @@
         "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
         "fillerId" : "http://purl.obolibrary.org/obo/SO_0000869"
       } ]
-    }, {
-      "definedClassId" : "http://purl.obolibrary.org/obo/SO_0000779",
-      "genusIds" : [ "http://purl.obolibrary.org/obo/SO_0000768" ],
-      "restrictions" : [ {
-        "propertyId" : "http://purl.obolibrary.org/obo/so#has_quality",
-        "fillerId" : "http://purl.obolibrary.org/obo/SO_0000783"
-      } ]
     } ],
     "domainRangeAxioms" : [ ],
     "propertyChainAxioms" : [ ]
   } ]
-}
+}
\ No newline at end of file

From d4dcd781c4f935aa6904ca0ffa722dfa15bffc2c Mon Sep 17 00:00:00 2001
From: Siddhartha Basu <biosidd@gmail.com>
Date: Mon, 14 Aug 2023 18:16:13 -0500
Subject: [PATCH 11/11] chore(lint.yaml): update runs-on value to
 'ubuntu-latest' and go-version to '1.20' for better compatibility and
 maintainability

The runs-on value is updated to 'ubuntu-latest' to ensure that the
workflow runs on the latest version of Ubuntu. The go-version is changed
to '1.20' to specify a more general version of Go, allowing for better
compatibility and easier maintenance of the workflow.
---
 .github/workflows/lint.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index b7102e2..0e1b26a 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -5,14 +5,14 @@ on:
       - master
 jobs:
   lint:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
       - name: check out code
         uses: actions/checkout@v3
       - name: set up golang
         uses: actions/setup-go@v4
         with:
-            go-version: 1.20.4
+            go-version: '1.20'
             cache: false
       - name: run linter
         uses: golangci/golangci-lint-action@v3