Merge pull request #98 from julesjacobsen/fixing-things

Change for #65 - add PropertyType to PROPERTY Nodes Change for #90 - ensure all declared nodes (CLASS, INDIVIDUAL, PROPERTY) are added even if unlabelled. Change for #93 - log untranslated axioms to WARN Update examples/ with changes Update schema/ with changes Enable obographs-cli to convert ttl to json and yaml Update for #103 - remove Guava dependency from core Update Junit to Jupiter 5.0.3 Update version to 0.3.1
geneontology · Nov 8, 2023 · 384641b · 384641b
2 parents f10fa43 + 4c30db1
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diff --git a/examples/abox.json b/examples/abox.json
@@ -2,20 +2,84 @@
   "graphs" : [ {
     "id" : "http://purl.obolibrary.org/obo/T",
     "nodes" : [ {
-      "id" : "http://purl.obolibrary.org/obo/T/f1",
-      "type" : "INDIVIDUAL"
+      "id" : "http://purl.obolibrary.org/obo/T/Female",
+      "type" : "CLASS"
     }, {
       "id" : "http://purl.obolibrary.org/obo/T/Male",
       "type" : "CLASS"
     }, {
-      "id" : "http://purl.obolibrary.org/obo/T/m1",
-      "type" : "INDIVIDUAL"
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/T/Female",
+      "id" : "http://purl.obolibrary.org/obo/T/Person",
       "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/ancestor-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/brother-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/child-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/descendant-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/father-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/genealogically-related-to",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/grandfather-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/grandmother-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/grandparent-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/mother-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/parent-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/sibling-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/sister-of",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT"
     }, {
       "id" : "http://purl.obolibrary.org/obo/T/b",
       "type" : "INDIVIDUAL"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/b1",
+      "type" : "INDIVIDUAL"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/b2",
+      "type" : "INDIVIDUAL"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/c",
+      "type" : "INDIVIDUAL"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/f1",
+      "type" : "INDIVIDUAL"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/T/m1",
+      "type" : "INDIVIDUAL"
     } ],
     "edges" : [ {
       "sub" : "http://purl.obolibrary.org/obo/T/Female",

diff --git a/examples/abox.yaml b/examples/abox.yaml
@@ -2,16 +2,63 @@
 graphs:
 - id: "http://purl.obolibrary.org/obo/T"
   nodes:
-  - id: "http://purl.obolibrary.org/obo/T/f1"
-    type: "INDIVIDUAL"
+  - id: "http://purl.obolibrary.org/obo/T/Female"
+    type: "CLASS"
   - id: "http://purl.obolibrary.org/obo/T/Male"
     type: "CLASS"
-  - id: "http://purl.obolibrary.org/obo/T/m1"
-    type: "INDIVIDUAL"
-  - id: "http://purl.obolibrary.org/obo/T/Female"
+  - id: "http://purl.obolibrary.org/obo/T/Person"
     type: "CLASS"
+  - id: "http://purl.obolibrary.org/obo/T/ancestor-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/brother-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/child-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/descendant-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/father-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/genealogically-related-to"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/grandfather-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/grandmother-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/grandparent-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/mother-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/parent-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/sibling-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+  - id: "http://purl.obolibrary.org/obo/T/sister-of"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
   - id: "http://purl.obolibrary.org/obo/T/b"
     type: "INDIVIDUAL"
+  - id: "http://purl.obolibrary.org/obo/T/b1"
+    type: "INDIVIDUAL"
+  - id: "http://purl.obolibrary.org/obo/T/b2"
+    type: "INDIVIDUAL"
+  - id: "http://purl.obolibrary.org/obo/T/c"
+    type: "INDIVIDUAL"
+  - id: "http://purl.obolibrary.org/obo/T/f1"
+    type: "INDIVIDUAL"
+  - id: "http://purl.obolibrary.org/obo/T/m1"
+    type: "INDIVIDUAL"
   edges:
   - sub: "http://purl.obolibrary.org/obo/T/Female"
     pred: "is_a"

diff --git a/examples/basic.json b/examples/basic.json
@@ -8,22 +8,6 @@
       } ]
     },
     "nodes" : [ {
-      "id" : "http://purl.obolibrary.org/obo/BFO_0000050",
-      "type" : "PROPERTY",
-      "meta" : {
-        "xrefs" : [ {
-          "val" : "BFO:0000050"
-        } ],
-        "basicPropertyValues" : [ {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
-          "val" : "part_of"
-        } ]
-      }
-    }, {
-      "id" : "http://purl.obolibrary.org/obo/IAO_0000115",
-      "lbl" : "definition",
-      "type" : "PROPERTY"
-    }, {
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002101",
       "lbl" : "limb",
       "type" : "CLASS"
@@ -44,14 +28,42 @@
       "id" : "http://purl.obolibrary.org/obo/UBERON_0002470",
       "lbl" : "autopod region",
       "type" : "CLASS"
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/BFO_0000050",
+      "type" : "PROPERTY",
+      "propertyType" : "OBJECT",
+      "meta" : {
+        "xrefs" : [ {
+          "val" : "BFO:0000050"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
+          "val" : "part_of"
+        } ]
+      }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/IAO_0000115",
+      "lbl" : "definition",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
       "lbl" : "database_cross_reference",
-      "type" : "PROPERTY"
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://www.geneontology.org/formats/oboInOwl#id",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
       "lbl" : "shorthand",
-      "type" : "PROPERTY"
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
+    }, {
+      "id" : "http://www.w3.org/2000/01/rdf-schema#label",
+      "type" : "PROPERTY",
+      "propertyType" : "ANNOTATION"
     } ],
     "edges" : [ {
       "sub" : "http://purl.obolibrary.org/obo/UBERON_0002102",

diff --git a/examples/basic.yaml b/examples/basic.yaml
@@ -6,17 +6,6 @@ graphs:
     - pred: "http://www.w3.org/2000/01/rdf-schema#comment"
       val: "test manus ontology"
   nodes:
-  - id: "http://purl.obolibrary.org/obo/BFO_0000050"
-    type: "PROPERTY"
-    meta:
-      xrefs:
-      - val: "BFO:0000050"
-      basicPropertyValues:
-      - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand"
-        val: "part_of"
-  - id: "http://purl.obolibrary.org/obo/IAO_0000115"
-    lbl: "definition"
-    type: "PROPERTY"
   - id: "http://purl.obolibrary.org/obo/UBERON_0002101"
     lbl: "limb"
     type: "CLASS"
@@ -32,12 +21,33 @@ graphs:
   - id: "http://purl.obolibrary.org/obo/UBERON_0002470"
     lbl: "autopod region"
     type: "CLASS"
+  - id: "http://purl.obolibrary.org/obo/BFO_0000050"
+    type: "PROPERTY"
+    propertyType: "OBJECT"
+    meta:
+      xrefs:
+      - val: "BFO:0000050"
+      basicPropertyValues:
+      - pred: "http://www.geneontology.org/formats/oboInOwl#shorthand"
+        val: "part_of"
+  - id: "http://purl.obolibrary.org/obo/IAO_0000115"
+    lbl: "definition"
+    type: "PROPERTY"
+    propertyType: "ANNOTATION"
   - id: "http://www.geneontology.org/formats/oboInOwl#hasDbXref"
     lbl: "database_cross_reference"
     type: "PROPERTY"
+    propertyType: "ANNOTATION"
+  - id: "http://www.geneontology.org/formats/oboInOwl#id"
+    type: "PROPERTY"
+    propertyType: "ANNOTATION"
   - id: "http://www.geneontology.org/formats/oboInOwl#shorthand"
     lbl: "shorthand"
     type: "PROPERTY"
+    propertyType: "ANNOTATION"
+  - id: "http://www.w3.org/2000/01/rdf-schema#label"
+    type: "PROPERTY"
+    propertyType: "ANNOTATION"
   edges:
   - sub: "http://purl.obolibrary.org/obo/UBERON_0002102"
     pred: "is_a"