Merge pull request #53 from geneontology/issue-38

Adding synonym type. Fixes #38
geneontology · Jan 22, 2020 · 3e09271 · 3e09271
2 parents 0f7f07e + 57ee209
commit 3e09271
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Showing 16 changed files with 713 additions and 671 deletions.
diff --git a/examples/basic.json b/examples/basic.json
@@ -4,10 +4,6 @@
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002470",
       "type" : "CLASS",
       "lbl" : "autopod region"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
-      "type" : "PROPERTY",
-      "lbl" : "shorthand"
     }, {
       "id" : "http://purl.obolibrary.org/obo/BFO_0000050",
       "meta" : {
@@ -20,6 +16,10 @@
         } ]
       },
       "type" : "PROPERTY"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
+      "type" : "PROPERTY",
+      "lbl" : "shorthand"
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
       "type" : "PROPERTY",
@@ -32,10 +32,6 @@
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002102",
       "type" : "CLASS",
       "lbl" : "forelimb"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/UBERON_0002101",
-      "type" : "CLASS",
-      "lbl" : "limb"
     }, {
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002398",
       "meta" : {
@@ -46,6 +42,10 @@
       },
       "type" : "CLASS",
       "lbl" : "manus"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0002101",
+      "type" : "CLASS",
+      "lbl" : "limb"
     } ],
     "edges" : [ {
       "sub" : "http://purl.obolibrary.org/obo/UBERON_0002102",

diff --git a/examples/basic.yaml b/examples/basic.yaml
@@ -4,9 +4,6 @@ graphs:
   - id: "http://purl.obolibrary.org/obo/UBERON_0002470"
     type: "CLASS"
     lbl: "autopod region"
-  - id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
-    type: "PROPERTY"
-    lbl: "shorthand"
   - id: "http://purl.obolibrary.org/obo/BFO_0000050"
     meta:
       xrefs:
@@ -15,6 +12,9 @@ graphs:
       - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand"
         val: "part_of"
     type: "PROPERTY"
+  - id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
+    type: "PROPERTY"
+    lbl: "shorthand"
   - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
     type: "PROPERTY"
     lbl: "database_cross_reference"
@@ -24,16 +24,16 @@ graphs:
   - id: "http://purl.obolibrary.org/obo/UBERON_0002102"
     type: "CLASS"
     lbl: "forelimb"
-  - id: "http://purl.obolibrary.org/obo/UBERON_0002101"
-    type: "CLASS"
-    lbl: "limb"
   - id: "http://purl.obolibrary.org/obo/UBERON_0002398"
     meta:
       definition:
         val: "."
         xrefs: []
     type: "CLASS"
     lbl: "manus"
+  - id: "http://purl.obolibrary.org/obo/UBERON_0002101"
+    type: "CLASS"
+    lbl: "limb"
   edges:
   - sub: "http://purl.obolibrary.org/obo/UBERON_0002102"
     pred: "is_a"

diff --git a/examples/equivNodeSetTest.json b/examples/equivNodeSetTest.json
@@ -9,35 +9,35 @@
         },
         "synonyms" : [ {
           "pred" : "hasExactSynonym",
-          "val" : "Hemangiosarcoma",
+          "val" : "hemangiosarcoma",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "HEMANGIOSARCOMA, MALIGNANT",
+          "val" : "Hemangiosarcoma",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "angiosarcoma",
+          "val" : "HEMANGIOSARCOMA, MALIGNANT",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Hemangiosarcoma",
+          "val" : "Malignant Angioendothelioma",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Angiosarcoma",
+          "val" : "Hemangiosarcoma",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "hemangiosarcoma",
+          "val" : "Malignant Hemangioendothelioma",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Malignant Angioendothelioma",
+          "val" : "angiosarcoma",
           "xrefs" : [ ]
         }, {
           "pred" : "hasExactSynonym",
-          "val" : "Malignant Hemangioendothelioma",
+          "val" : "Angiosarcoma",
           "xrefs" : [ ]
         } ]
       },
@@ -80,10 +80,6 @@
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
       "type" : "PROPERTY",
       "lbl" : "database_cross_reference"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/IAO_0000115",
-      "type" : "PROPERTY",
-      "lbl" : "definition"
     }, {
       "id" : "http://purl.obolibrary.org/obo/DOID_267",
       "meta" : {
@@ -97,6 +93,10 @@
         "deprecated" : true
       },
       "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/IAO_0000115",
+      "type" : "PROPERTY",
+      "lbl" : "definition"
     }, {
       "id" : "http://purl.obolibrary.org/obo/DOID_0001816",
       "meta" : {
@@ -106,23 +106,23 @@
         },
         "subsets" : [ "http://purl.obolibrary.org/obo/TEMP#NCIthesaurus" ],
         "xrefs" : [ {
-          "val" : "SCTID:33176006"
+          "val" : "MESH:D006394"
         }, {
-          "val" : "UMLS:C0018923"
+          "val" : "NCIT:C9275"
         }, {
-          "val" : "Orphanet:263413"
+          "val" : "SCTID:33176006"
         }, {
           "val" : "SCTID:39000009"
         }, {
-          "val" : "MESH:D006394"
-        }, {
-          "val" : "UMLS:C0854893"
+          "val" : "UMLS:C0018923"
         }, {
           "val" : "SCTID:403977003"
         }, {
-          "val" : "NCIT:C9275"
+          "val" : "UMLS:C0854893"
         }, {
           "val" : "NCIT:C3088"
+        }, {
+          "val" : "Orphanet:263413"
         } ],
         "synonyms" : [ {
           "pred" : "hasExactSynonym",

diff --git a/examples/equivNodeSetTest.yaml b/examples/equivNodeSetTest.yaml
@@ -12,29 +12,29 @@ graphs:
           \ lymphedema are at increased risk of developing angiosarcoma."
         xrefs: []
       synonyms:
+      - pred: "hasExactSynonym"
+        val: "hemangiosarcoma"
+        xrefs: []
       - pred: "hasExactSynonym"
         val: "Hemangiosarcoma"
         xrefs: []
       - pred: "hasExactSynonym"
         val: "HEMANGIOSARCOMA, MALIGNANT"
         xrefs: []
       - pred: "hasExactSynonym"
-        val: "angiosarcoma"
+        val: "Malignant Angioendothelioma"
         xrefs: []
       - pred: "hasExactSynonym"
         val: "Hemangiosarcoma"
         xrefs: []
       - pred: "hasExactSynonym"
-        val: "Angiosarcoma"
-        xrefs: []
-      - pred: "hasExactSynonym"
-        val: "hemangiosarcoma"
+        val: "Malignant Hemangioendothelioma"
         xrefs: []
       - pred: "hasExactSynonym"
-        val: "Malignant Angioendothelioma"
+        val: "angiosarcoma"
         xrefs: []
       - pred: "hasExactSynonym"
-        val: "Malignant Hemangioendothelioma"
+        val: "Angiosarcoma"
         xrefs: []
     type: "CLASS"
     lbl: "Angiosarcoma"
@@ -67,9 +67,6 @@ graphs:
   - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
     type: "PROPERTY"
     lbl: "database_cross_reference"
-  - id: "http://purl.obolibrary.org/obo/IAO_0000115"
-    type: "PROPERTY"
-    lbl: "definition"
   - id: "http://purl.obolibrary.org/obo/DOID_267"
     meta:
       basicPropertyValues:
@@ -79,6 +76,9 @@ graphs:
         val: "http://purl.obolibrary.org/obo/IAO_0000227"
       deprecated: true
     type: "CLASS"
+  - id: "http://purl.obolibrary.org/obo/IAO_0000115"
+    type: "PROPERTY"
+    lbl: "definition"
   - id: "http://purl.obolibrary.org/obo/DOID_0001816"
     meta:
       definition:
@@ -92,15 +92,15 @@ graphs:
       subsets:
       - "http://purl.obolibrary.org/obo/TEMP#NCIthesaurus"
       xrefs:
+      - val: "MESH:D006394"
+      - val: "NCIT:C9275"
       - val: "SCTID:33176006"
-      - val: "UMLS:C0018923"
-      - val: "Orphanet:263413"
       - val: "SCTID:39000009"
-      - val: "MESH:D006394"
-      - val: "UMLS:C0854893"
+      - val: "UMLS:C0018923"
       - val: "SCTID:403977003"
-      - val: "NCIT:C9275"
+      - val: "UMLS:C0854893"
       - val: "NCIT:C3088"
+      - val: "Orphanet:263413"
       synonyms:
       - pred: "hasExactSynonym"
         val: "hemangiosarcoma"

diff --git a/examples/logicalDefinitionTest.json b/examples/logicalDefinitionTest.json
@@ -4,10 +4,6 @@
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002470",
       "type" : "CLASS",
       "lbl" : "autopod region"
-    }, {
-      "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
-      "type" : "PROPERTY",
-      "lbl" : "shorthand"
     }, {
       "id" : "http://purl.obolibrary.org/obo/BFO_0000050",
       "meta" : {
@@ -20,6 +16,10 @@
         } ]
       },
       "type" : "PROPERTY"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
+      "type" : "PROPERTY",
+      "lbl" : "shorthand"
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
       "type" : "PROPERTY",
@@ -32,10 +32,6 @@
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002102",
       "type" : "CLASS",
       "lbl" : "forelimb"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/UBERON_0002101",
-      "type" : "CLASS",
-      "lbl" : "limb"
     }, {
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002398",
       "meta" : {
@@ -46,6 +42,10 @@
       },
       "type" : "CLASS",
       "lbl" : "manus"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/UBERON_0002101",
+      "type" : "CLASS",
+      "lbl" : "limb"
     } ],
     "edges" : [ {
       "sub" : "http://purl.obolibrary.org/obo/UBERON_0002102",

diff --git a/examples/logicalDefinitionTest.yaml b/examples/logicalDefinitionTest.yaml
@@ -4,9 +4,6 @@ graphs:
   - id: "http://purl.obolibrary.org/obo/UBERON_0002470"
     type: "CLASS"
     lbl: "autopod region"
-  - id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
-    type: "PROPERTY"
-    lbl: "shorthand"
   - id: "http://purl.obolibrary.org/obo/BFO_0000050"
     meta:
       xrefs:
@@ -15,6 +12,9 @@ graphs:
       - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand"
         val: "part_of"
     type: "PROPERTY"
+  - id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
+    type: "PROPERTY"
+    lbl: "shorthand"
   - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
     type: "PROPERTY"
     lbl: "database_cross_reference"
@@ -24,16 +24,16 @@ graphs:
   - id: "http://purl.obolibrary.org/obo/UBERON_0002102"
     type: "CLASS"
     lbl: "forelimb"
-  - id: "http://purl.obolibrary.org/obo/UBERON_0002101"
-    type: "CLASS"
-    lbl: "limb"
   - id: "http://purl.obolibrary.org/obo/UBERON_0002398"
     meta:
       definition:
         val: "."
         xrefs: []
     type: "CLASS"
     lbl: "manus"
+  - id: "http://purl.obolibrary.org/obo/UBERON_0002101"
+    type: "CLASS"
+    lbl: "limb"
   edges:
   - sub: "http://purl.obolibrary.org/obo/UBERON_0002102"
     pred: "is_a"