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obophenotype · Jul 29, 2017 · bcd5c5a · bcd5c5a
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diff --git a/cl-basic.obo b/cl-basic.obo
@@ -4464,6 +4464,8 @@ name: cardiac muscle myoblast
 namespace: cell
 alt_id: CL:0000714
 def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:A11.635.470]
+synonym: "cardiac muscle progenitor cell" EXACT []
+synonym: "cardiomyocyte progenitor cell" EXACT []
 xref: FMA:84797
 is_a: CL:0002494 ! cardiocyte
 is_a: CL:0010021 ! cardiac myoblast
@@ -9698,11 +9700,11 @@ id: CL:0001044
 name: effector CD4-positive, alpha-beta T cell
 namespace: cell
 def: "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." [GOC:add, PMID:22343568]
+comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.
 synonym: "effector CD4+ T cell" BROAD [PMID:22343568]
 synonym: "effector CD4-positive, alpha-beta T lymphocyte" EXACT []
 synonym: "effector CD4-positive, alpha-beta T-cell" EXACT []
 synonym: "effector CD4-positive, alpha-beta T-lymphocyte" EXACT []
-synonym: "This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy." EXACT []
 is_a: CL:0000624 ! CD4-positive, alpha-beta T cell
 is_a: CL:0000911 ! effector T cell
 
@@ -10001,8 +10003,8 @@ is_a: CL:0000136 ! fat cell
 [Term]
 id: CL:0001071
 name: group 3 innate lymphoid cell
-namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"}
 namespace: cell
+def: "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
 synonym: "ILC3" EXACT []
 is_a: CL:0001065 ! innate lymphoid cell
 property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
@@ -22361,10 +22363,6 @@ is_a: CL:2000029 ! central nervous system neuron
 created_by: TermGenie
 creation_date: 2015-12-03T16:42:40Z
 
-[Typedef]
-id: RO:0002161
-name: never in taxon
-
 [Typedef]
 id: has_completed
 name: has_completed

diff --git a/cl-basic.owl b/cl-basic.owl
@@ -341,14 +341,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/RO_0002161 -->
-
-    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002161">
-        <rdfs:label>never in taxon</rdfs:label>
-    </owl:ObjectProperty>
-
-
-
     <!-- http://purl.obolibrary.org/obo/cl#has_completed -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/cl#has_completed">
@@ -9417,6 +9409,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A precursor cell destined to differentiate into cardiac muscle cell.</obo:IAO_0000115>
         <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL:0000714</oboInOwl:hasAlternativeId>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:84797</oboInOwl:hasDbXref>
+        <oboInOwl:hasExactSynonym>cardiac muscle progenitor cell</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>cardiomyocyte progenitor cell</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cardiac muscle myoblast</rdfs:label>
     </owl:Class>
@@ -20950,11 +20944,11 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000911"/>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive.</obo:IAO_0000115>
         <oboInOwl:hasBroadSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4+ T cell</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T lymphocyte</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-cell</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-lymphocyte</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</rdfs:comment>
         <rdfs:label>effector CD4-positive, alpha-beta T cell</rdfs:label>
     </owl:Class>
     <owl:Axiom>
@@ -21702,16 +21696,16 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/CL_0001071">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0001065"/>
+        <obo:IAO_0000115>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</obo:IAO_0000115>
         <dc:creator rdf:resource="http://orcid.org/0000-0001-9990-8331"/>
         <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-01-31T20:21:26Z</dc:date>
         <oboInOwl:hasExactSynonym>ILC3</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</oboInOwl:hasOBONamespace>
         <oboInOwl:hasOBONamespace>cell</oboInOwl:hasOBONamespace>
         <rdfs:label>group 3 innate lymphoid cell</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0001071"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:add</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:dsd</oboInOwl:hasDbXref>

diff --git a/cl.obo b/cl.obo
@@ -1,5 +1,5 @@
 format-version: 1.2
-data-version: releases/2017-04-14
+data-version: releases/2017-07-29
 subsetdef: ubprop:upper_level "abstract upper-level terms not directly useful for analysis"
 synonymtypedef: HUMAN_PREFERRED "preferred term when talking about an instance of this class in Homo sapiens"
 synonymtypedef: LATIN "latin term"
@@ -2140,13 +2140,10 @@ xref: VHOG:0001679
 is_a: CL:0000147 {is_inferred="true"} ! pigment cell
 is_a: CL:0002371 ! somatic cell
 intersection_of: CL:0000147 ! pigment cell
-intersection_of: CL:0000147 ! pigment cell
 intersection_of: develops_from CL:0000541 ! melanoblast
 intersection_of: has_part GO:0042470 ! melanosome
-intersection_of: never_in_taxon NCBITaxon:6237 ! Caenorhabditis
 relationship: develops_from CL:0000541 ! melanoblast
 relationship: has_part GO:0042470 ! melanosome
-relationship: never_in_taxon NCBITaxon:6237 ! Caenorhabditis
 
 [Term]
 id: CL:0000149
@@ -5511,6 +5508,8 @@ name: cardiac muscle myoblast
 namespace: cell
 alt_id: CL:0000714
 def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:A11.635.470]
+synonym: "cardiac muscle progenitor cell" EXACT []
+synonym: "cardiomyocyte progenitor cell" EXACT []
 xref: FMA:84797
 is_a: CL:0002494 ! cardiocyte
 is_a: CL:0010021 ! cardiac myoblast
@@ -13531,11 +13530,11 @@ id: CL:0001044
 name: effector CD4-positive, alpha-beta T cell
 namespace: cell
 def: "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." [GOC:add, PMID:22343568]
+comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.
 synonym: "effector CD4+ T cell" BROAD [PMID:22343568]
 synonym: "effector CD4-positive, alpha-beta T lymphocyte" EXACT []
 synonym: "effector CD4-positive, alpha-beta T-cell" EXACT []
 synonym: "effector CD4-positive, alpha-beta T-lymphocyte" EXACT []
-synonym: "This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy." EXACT []
 is_a: CL:0000624 ! CD4-positive, alpha-beta T cell
 is_a: CL:0000911 ! effector T cell
 intersection_of: CL:0000911 ! effector T cell
@@ -14021,8 +14020,8 @@ relationship: part_of UBERON:0001347 ! white adipose tissue
 [Term]
 id: CL:0001071
 name: group 3 innate lymphoid cell
-namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"}
 namespace: cell
+def: "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
 synonym: "ILC3" EXACT []
 is_a: CL:0001065 ! innate lymphoid cell
 intersection_of: CL:0001065 ! innate lymphoid cell
@@ -75681,11 +75680,6 @@ xref: RO:0002212
 is_a: regulates ! regulates
 inverse_of: negatively_regulated_by ! negatively regulated by
 
-[Typedef]
-id: never_in_taxon
-name: never in taxon
-xref: RO:0002161
-
 [Typedef]
 id: occurs_in
 name: occurs in

diff --git a/cl.owl b/cl.owl
@@ -12,7 +12,7 @@
      xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:dc="http://purl.org/dc/elements/1.1/">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cl.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2017-04-14/cl.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/cl/releases/2017-07-29/cl.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl/imports/pato_import.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl/imports/clo_import.owl"/>
         <owl:imports rdf:resource="http://purl.obolibrary.org/obo/cl/imports/ro_import.owl"/>
@@ -373,14 +373,6 @@
 
 
 
-    <!-- http://purl.obolibrary.org/obo/RO_0002161 -->
-
-    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002161">
-        <rdfs:label>never in taxon</rdfs:label>
-    </owl:ObjectProperty>
-
-
-
     <!-- http://purl.obolibrary.org/obo/RO_0002211 -->
 
     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002211">
@@ -6062,17 +6054,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <owl:equivalentClass>
-            <owl:Class>
-                <owl:intersectionOf rdf:parseType="Collection">
-                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/CL_0000147"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002161"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_6237"/>
-                    </owl:Restriction>
-                </owl:intersectionOf>
-            </owl:Class>
-        </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0000147"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CL_0002371"/>
         <rdfs:subClassOf>
@@ -6081,12 +6062,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0042470"/>
             </owl:Restriction>
         </rdfs:subClassOf>
-        <rdfs:subClassOf>
-            <owl:Restriction>
-                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002161"/>
-                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_6237"/>
-            </owl:Restriction>
-        </rdfs:subClassOf>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002202"/>
@@ -14600,6 +14575,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A precursor cell destined to differentiate into cardiac muscle cell.</obo:IAO_0000115>
         <oboInOwl:hasAlternativeId rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL:0000714</oboInOwl:hasAlternativeId>
         <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FMA:84797</oboInOwl:hasDbXref>
+        <oboInOwl:hasExactSynonym>cardiac muscle progenitor cell</oboInOwl:hasExactSynonym>
+        <oboInOwl:hasExactSynonym>cardiomyocyte progenitor cell</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
         <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cardiac muscle myoblast</rdfs:label>
     </owl:Class>
@@ -42428,11 +42405,11 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
         </rdfs:subClassOf>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive.</obo:IAO_0000115>
         <oboInOwl:hasBroadSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4+ T cell</oboInOwl:hasBroadSynonym>
-        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T lymphocyte</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-cell</oboInOwl:hasExactSynonym>
         <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">effector CD4-positive, alpha-beta T-lymphocyte</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">cell</oboInOwl:hasOBONamespace>
+        <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This cell type is compatible with the HIPC Lyoplate markers for &apos;effector CD4+ T cell&apos;.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.</rdfs:comment>
         <rdfs:label>effector CD4-positive, alpha-beta T cell</rdfs:label>
     </owl:Class>
     <owl:Axiom>
@@ -44139,16 +44116,16 @@ radial glial cells acting as neural progenitors throughout life.</rdfs:comment>
                 <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PR_000003455"/>
             </owl:Restriction>
         </rdfs:subClassOf>
+        <obo:IAO_0000115>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</obo:IAO_0000115>
         <dc:creator rdf:resource="http://orcid.org/0000-0001-9990-8331"/>
         <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-01-31T20:21:26Z</dc:date>
         <oboInOwl:hasExactSynonym>ILC3</oboInOwl:hasExactSynonym>
-        <oboInOwl:hasOBONamespace>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</oboInOwl:hasOBONamespace>
         <oboInOwl:hasOBONamespace>cell</oboInOwl:hasOBONamespace>
         <rdfs:label>group 3 innate lymphoid cell</rdfs:label>
     </owl:Class>
     <owl:Axiom>
         <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/CL_0001071"/>
-        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
         <owl:annotatedTarget>An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22.</owl:annotatedTarget>
         <oboInOwl:hasDbXref>GOC:add</oboInOwl:hasDbXref>
         <oboInOwl:hasDbXref>GOC:dsd</oboInOwl:hasDbXref>

diff --git a/src/ontology/cl-basic.obo b/src/ontology/cl-basic.obo
@@ -4464,6 +4464,8 @@ name: cardiac muscle myoblast
 namespace: cell
 alt_id: CL:0000714
 def: "A precursor cell destined to differentiate into cardiac muscle cell." [GOC:tfm, MESH:A11.635.470]
+synonym: "cardiac muscle progenitor cell" EXACT []
+synonym: "cardiomyocyte progenitor cell" EXACT []
 xref: FMA:84797
 is_a: CL:0002494 ! cardiocyte
 is_a: CL:0010021 ! cardiac myoblast
@@ -9698,11 +9700,11 @@ id: CL:0001044
 name: effector CD4-positive, alpha-beta T cell
 namespace: cell
 def: "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." [GOC:add, PMID:22343568]
+comment: This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy.
 synonym: "effector CD4+ T cell" BROAD [PMID:22343568]
 synonym: "effector CD4-positive, alpha-beta T lymphocyte" EXACT []
 synonym: "effector CD4-positive, alpha-beta T-cell" EXACT []
 synonym: "effector CD4-positive, alpha-beta T-lymphocyte" EXACT []
-synonym: "This cell type is compatible with the HIPC Lyoplate markers for 'effector CD4+ T cell'.  The functional characteristics of this cell type currently undefined in CL, which affects its proper placement within the hierarchy." EXACT []
 is_a: CL:0000624 ! CD4-positive, alpha-beta T cell
 is_a: CL:0000911 ! effector T cell
 
@@ -10001,8 +10003,8 @@ is_a: CL:0000136 ! fat cell
 [Term]
 id: CL:0001071
 name: group 3 innate lymphoid cell
-namespace: An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. {xref="GOC:add", xref="GOC:dsd", xref="PMID:23348417", xref="PMID:23292121"}
 namespace: cell
+def: "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417]
 synonym: "ILC3" EXACT []
 is_a: CL:0001065 ! innate lymphoid cell
 property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331
@@ -22361,10 +22363,6 @@ is_a: CL:2000029 ! central nervous system neuron
 created_by: TermGenie
 creation_date: 2015-12-03T16:42:40Z
 
-[Typedef]
-id: RO:0002161
-name: never in taxon
-
 [Typedef]
 id: has_completed
 name: has_completed