Merge pull request #17 from geneontology/issue-13

Mapping owl:deprecated
geneontology · Jan 9, 2017 · 8af1afa · 8af1afa
2 parents 58789be + 49ef973
commit 8af1afa
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Showing 12 changed files with 120 additions and 105 deletions.
diff --git a/examples/equivNodeSetTest.json b/examples/equivNodeSetTest.json
@@ -88,15 +88,13 @@
       "id" : "http://purl.obolibrary.org/obo/DOID_267",
       "meta" : {
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "http://purl.obolibrary.org/obo/DOID_0001816"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
           "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS"
     }, {
@@ -151,13 +149,11 @@
         "basicPropertyValues" : [ {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "http://purl.obolibrary.org/obo/DOID_0001816"
-        }, {
-          "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"
     } ],

diff --git a/examples/equivNodeSetTest.yaml b/examples/equivNodeSetTest.yaml
@@ -73,12 +73,11 @@ graphs:
   - id: "http://purl.obolibrary.org/obo/DOID_267"
     meta:
       basicPropertyValues:
-      - pred: "http://www.w3.org/2002/07/owl#deprecated"
-        val: "true"
       - pred: "http://purl.obolibrary.org/obo/IAO_0100001"
         val: "http://purl.obolibrary.org/obo/DOID_0001816"
       - 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/DOID_0001816"
     meta:
@@ -121,10 +120,9 @@ graphs:
       basicPropertyValues:
       - pred: "http://purl.obolibrary.org/obo/IAO_0100001"
         val: "http://purl.obolibrary.org/obo/DOID_0001816"
-      - 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"
   edges:
   - sub: "http://purl.obolibrary.org/obo/NCIT_C3088"

diff --git a/examples/nucleus.json b/examples/nucleus.json
@@ -196,10 +196,8 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000231",
           "val" : "http://purl.obolibrary.org/obo/IAO_0000227"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS"
     }, {

diff --git a/examples/nucleus.yaml b/examples/nucleus.yaml
@@ -202,8 +202,7 @@ graphs:
         val: "http://purl.obolibrary.org/obo/GO_0005575"
       - pred: "http://purl.obolibrary.org/obo/IAO_0000231"
         val: "http://purl.obolibrary.org/obo/IAO_0000227"
-      - pred: "http://www.w3.org/2002/07/owl#deprecated"
-        val: "true"
+      deprecated: true
     type: "CLASS"
   - id: "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"
     type: "PROPERTY"

diff --git a/examples/obsoletion_example.json b/examples/obsoletion_example.json
@@ -4,15 +4,13 @@
       "id" : "http://purl.obolibrary.org/obo/Y_2",
       "meta" : {
         "basicPropertyValues" : [ {
-          "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"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "http://purl.obolibrary.org/obo/Y_1"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS"
     }, {
@@ -38,10 +36,8 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0100001",
           "val" : "X:1"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "obsolete x2"

diff --git a/examples/obsoletion_example.yaml b/examples/obsoletion_example.yaml
@@ -4,12 +4,11 @@ graphs:
   - id: "http://purl.obolibrary.org/obo/Y_2"
     meta:
       basicPropertyValues:
-      - 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"
       - pred: "http://purl.obolibrary.org/obo/IAO_0100001"
         val: "http://purl.obolibrary.org/obo/Y_1"
+      deprecated: true
     type: "CLASS"
   - id: "http://purl.obolibrary.org/obo/IAO_0100001"
     type: "PROPERTY"
@@ -28,8 +27,7 @@ graphs:
         val: "x"
       - pred: "http://purl.obolibrary.org/obo/IAO_0100001"
         val: "X:1"
-      - pred: "http://www.w3.org/2002/07/owl#deprecated"
-        val: "true"
+      deprecated: true
     type: "CLASS"
     lbl: "obsolete x2"
   - id: "http://purl.obolibrary.org/obo/Y_1"

diff --git a/examples/ro.json b/examples/ro.json
@@ -7437,10 +7437,8 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Chris Mungall"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "PROPERTY",
       "lbl" : "obsolete has indirect input"
@@ -7469,49 +7467,47 @@
       "type" : "PROPERTY",
       "lbl" : "in_subset"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002402",
+      "id" : "http://purl.obolibrary.org/obo/RO_0002523",
       "meta" : {
         "definition" : {
-          "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. ",
+          "val" : "inverse of bounds sequence of",
           "xrefs" : [ ]
         },
+        "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "directly produces"
+          "pred" : "http://purl.org/spar/cito/citesAsAuthority",
+          "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Chris Mungall"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
-          "val" : "translation SubClassOf has_direct_output some protein"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
-          "val" : "http://purl.obolibrary.org/obo/IAO_0000428"
         } ]
       },
       "type" : "PROPERTY",
-      "lbl" : "obsolete has direct output"
+      "lbl" : "is bound by sequence of"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/RO_0002523",
+      "id" : "http://purl.obolibrary.org/obo/RO_0002402",
       "meta" : {
         "definition" : {
-          "val" : "inverse of bounds sequence of",
+          "val" : "p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. ",
           "xrefs" : [ ]
         },
-        "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.org/spar/cito/citesAsAuthority",
-          "val" : "http://biorxiv.org/content/early/2014/06/27/006650.abstract"
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
+          "val" : "directly produces"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Chris Mungall"
-        } ]
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
+          "val" : "translation SubClassOf has_direct_output some protein"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
+          "val" : "http://purl.obolibrary.org/obo/IAO_0000428"
+        } ],
+        "deprecated" : true
       },
       "type" : "PROPERTY",
-      "lbl" : "is bound by sequence of"
+      "lbl" : "obsolete has direct output"
     }, {
       "id" : "http://purl.obolibrary.org/obo/RO_0002524",
       "meta" : {
@@ -7541,16 +7537,14 @@
         "basicPropertyValues" : [ {
           "pred" : "http://www.w3.org/2000/01/rdf-schema#comment",
           "val" : "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit"
-        }, {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
           "val" : "Chris Mungall"
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000114",
           "val" : "http://purl.obolibrary.org/obo/IAO_0000428"
-        } ]
+        } ],
+        "deprecated" : true
       },
       "type" : "PROPERTY",
       "lbl" : "obsolete has indirect output"
@@ -11205,10 +11199,7 @@
           "val" : "A continuant  that is either dependent on one or other independent continuant  bearers or inheres in or is borne by other entities.",
           "xrefs" : [ ]
         },
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.w3.org/2002/07/owl#deprecated",
-          "val" : "true"
-        } ]
+        "deprecated" : true
       },
       "type" : "CLASS",
       "lbl" : "obsolete dependent continuant"
@@ -14337,13 +14328,13 @@
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002207",
       "allValuesFromEdges" : [ {
-        "sub" : "http://purl.obolibrary.org/obo/CL_0000000",
-        "pred" : "http://purl.obolibrary.org/obo/RO_0002207",
-        "obj" : "http://purl.obolibrary.org/obo/CL_0000000"
-      }, {
         "sub" : "http://purl.obolibrary.org/obo/CARO_0010000",
         "pred" : "http://purl.obolibrary.org/obo/RO_0002207",
         "obj" : "http://purl.obolibrary.org/obo/CARO_0010000"
+      }, {
+        "sub" : "http://purl.obolibrary.org/obo/CL_0000000",
+        "pred" : "http://purl.obolibrary.org/obo/RO_0002207",
+        "obj" : "http://purl.obolibrary.org/obo/CL_0000000"
       } ]
     }, {
       "predicateId" : "http://purl.obolibrary.org/obo/RO_0002009",

diff --git a/examples/ro.yaml b/examples/ro.yaml
@@ -6248,8 +6248,7 @@ graphs:
         val: "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit"
       - pred: "http://purl.obolibrary.org/obo/IAO_0000117"
         val: "Chris Mungall"
-      - pred: "http://www.w3.org/2002/07/owl#deprecated"
-        val: "true"
+      deprecated: true
     type: "PROPERTY"
     lbl: "obsolete has indirect input"
   - id: "http://purl.obolibrary.org/obo/RO_0002522"
@@ -6274,15 +6273,27 @@ graphs:
   - id: "http://www.geneontology.org/formats/oboInOwl#inSubset"
     type: "PROPERTY"
     lbl: "in_subset"
+  - id: "http://purl.obolibrary.org/obo/RO_0002523"
+    meta:
+      definition:
+        val: "inverse of bounds sequence of"
+        xrefs: []
+      subsets:
+      - "http://purl.obolibrary.org/obo/RO_0002259"
+      basicPropertyValues:
+      - pred: "http://purl.org/spar/cito/citesAsAuthority"
+        val: "http://biorxiv.org/content/early/2014/06/27/006650.abstract"
+      - pred: "http://purl.obolibrary.org/obo/IAO_0000117"
+        val: "Chris Mungall"
+    type: "PROPERTY"
+    lbl: "is bound by sequence of"
   - id: "http://purl.obolibrary.org/obo/RO_0002402"
     meta:
       definition:
         val: "p has direct input c iff c is a participanti n p, c is present at the\
           \ end of p, and c is not present at the beginning of c. "
         xrefs: []
       basicPropertyValues:
-      - pred: "http://www.w3.org/2002/07/owl#deprecated"
-        val: "true"
       - pred: "http://purl.obolibrary.org/obo/IAO_0000118"
         val: "directly produces"
       - pred: "http://purl.obolibrary.org/obo/IAO_0000117"
@@ -6291,22 +6302,9 @@ graphs:
         val: "translation SubClassOf has_direct_output some protein"
       - pred: "http://purl.obolibrary.org/obo/IAO_0000114"
         val: "http://purl.obolibrary.org/obo/IAO_0000428"
+      deprecated: true
     type: "PROPERTY"
     lbl: "obsolete has direct output"
-  - id: "http://purl.obolibrary.org/obo/RO_0002523"
-    meta:
-      definition:
-        val: "inverse of bounds sequence of"
-        xrefs: []
-      subsets:
-      - "http://purl.obolibrary.org/obo/RO_0002259"
-      basicPropertyValues:
-      - pred: "http://purl.org/spar/cito/citesAsAuthority"
-        val: "http://biorxiv.org/content/early/2014/06/27/006650.abstract"
-      - pred: "http://purl.obolibrary.org/obo/IAO_0000117"
-        val: "Chris Mungall"
-    type: "PROPERTY"
-    lbl: "is bound by sequence of"
   - id: "http://purl.obolibrary.org/obo/RO_0002524"
     meta:
       definition:
@@ -6329,12 +6327,11 @@ graphs:
       basicPropertyValues:
       - pred: "http://www.w3.org/2000/01/rdf-schema#comment"
         val: "Likely to be obsoleted. See:\nhttps://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit"
-      - pred: "http://www.w3.org/2002/07/owl#deprecated"
-        val: "true"
       - pred: "http://purl.obolibrary.org/obo/IAO_0000117"
         val: "Chris Mungall"
       - pred: "http://purl.obolibrary.org/obo/IAO_0000114"
         val: "http://purl.obolibrary.org/obo/IAO_0000428"
+      deprecated: true
     type: "PROPERTY"
     lbl: "obsolete has indirect output"
   - id: "http://purl.obolibrary.org/obo/RO_0002408"
@@ -9441,9 +9438,7 @@ graphs:
         val: "A continuant  that is either dependent on one or other independent continuant\
           \  bearers or inheres in or is borne by other entities."
         xrefs: []
-      basicPropertyValues:
-      - pred: "http://www.w3.org/2002/07/owl#deprecated"
-        val: "true"
+      deprecated: true
     type: "CLASS"
     lbl: "obsolete dependent continuant"
   - id: "http://purl.obolibrary.org/obo/RO_0002088"
@@ -11854,12 +11849,12 @@ graphs:
     - "http://purl.obolibrary.org/obo/BFO_0000004"
   - predicateId: "http://purl.obolibrary.org/obo/RO_0002207"
     allValuesFromEdges:
-    - sub: "http://purl.obolibrary.org/obo/CL_0000000"
-      pred: "http://purl.obolibrary.org/obo/RO_0002207"
-      obj: "http://purl.obolibrary.org/obo/CL_0000000"
     - sub: "http://purl.obolibrary.org/obo/CARO_0010000"
       pred: "http://purl.obolibrary.org/obo/RO_0002207"
       obj: "http://purl.obolibrary.org/obo/CARO_0010000"
+    - sub: "http://purl.obolibrary.org/obo/CL_0000000"
+      pred: "http://purl.obolibrary.org/obo/RO_0002207"
+      obj: "http://purl.obolibrary.org/obo/CL_0000000"
   - predicateId: "http://purl.obolibrary.org/obo/RO_0002009"
     domainClassIds:
     - "http://purl.obolibrary.org/obo/CL_0000000"

diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.geneontology</groupId>
   <artifactId>obographs</artifactId>
-  <version>0.0.7</version>
+  <version>0.0.8</version>
   <packaging>jar</packaging>
   <name>${project.groupId}:${project.artifactId}</name>
   <description>Reference implementation for Obo Graphs</description>