Merge pull request #3 from brain-bican/ontology_url

Symbols added

mbao-simple.json

@@ -3,20 +3,26 @@
     "id" : "https://purl.brain-bican.org/ontology/mbao/mbao-simple.json",
     "meta" : {
       "basicPropertyValues" : [ {
+        "pred" : "http://purl.obolibrary.org/obo/IAO_0000700",
+        "val" : "https://purl.brain-bican.org/ontology/mbao/MBA_997"
+      }, {
+        "pred" : "http://purl.org/dc/terms/description",
+        "val" : "An application ontology built by combining ontologised versions of the Allen Institute Mouse Brain Atlas (MBA) StructureGraph mapped to Uberon."
+      }, {
         "pred" : "http://purl.org/dc/terms/license",
         "val" : "http://creativecommons.org/licenses/by/4.0/"
       }, {
         "pred" : "http://purl.org/dc/terms/title",
         "val" : "Mouse Brain Atlas Ontology"
       }, {
         "pred" : "http://www.w3.org/2002/07/owl#versionInfo",
-        "val" : "2023-08-25"
+        "val" : "2025-02-10"
       } ],
-      "version" : "https://purl.brain-bican.org/ontology/mbao/releases/2023-08-25/mbao-simple.json"
+      "version" : "https://purl.brain-bican.org/ontology/mbao/releases/2025-02-10/mbao-simple.json"
     },
     "nodes" : [ {
       "id" : "http://purl.obolibrary.org/obo/BFO_0000050",
-      "lbl" : "part_of",
+      "lbl" : "part of",
       "type" : "PROPERTY",
       "meta" : {
         "definition" : {
@@ -27,9 +33,6 @@
           "val" : "BFO:0000050"
         } ],
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000111",
-          "val" : "is part of"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
           "val" : "my brain is part of my body (continuant parthood, two material entities)"
         }, {
@@ -47,39 +50,6 @@
         }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000116",
           "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000118",
-          "val" : "part_of"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0001900",
-          "val" : "http://purl.obolibrary.org/obo/RO_0001901"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000002"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000003"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000004"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000017"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000019"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000020"
-        }, {
-          "pred" : "http://purl.obolibrary.org/obo/RO_0040042",
-          "val" : "http://purl.obolibrary.org/obo/BFO_0000031"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "external"
-        }, {
-          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
-          "val" : "quality"
         }, {
           "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
           "val" : "spatial"
@@ -103,6 +73,28 @@
           "val" : "https://wiki.geneontology.org/Part_of"
         } ]
       }
+    }, {
+      "id" : "http://purl.obolibrary.org/obo/IAO_0000700",
+      "lbl" : "has ontology root term",
+      "type" : "PROPERTY",
+      "meta" : {
+        "definition" : {
+          "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."
+        },
+        "xrefs" : [ {
+          "val" : "IAO:0000700"
+        } ],
+        "basicPropertyValues" : [ {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+          "val" : "uberon"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag",
+          "val" : "true"
+        }, {
+          "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
+          "val" : "has_ontology_root_term"
+        } ]
+      }
     }, {
       "id" : "http://purl.org/dc/terms/description",
       "lbl" : "description",
@@ -132,8 +124,23 @@
       "type" : "PROPERTY"
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasDbXref",
-      "lbl" : "database_cross_reference",
-      "type" : "PROPERTY"
+      "lbl" : "has cross-reference",
+      "type" : "PROPERTY",
+      "meta" : {
+        "definition" : {
+          "val" : "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI."
+        },
+        "basicPropertyValues" : [ {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000112",
+          "val" : "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string"
+        }, {
+          "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
+          "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/123"
+        }, {
+          "pred" : "http://purl.org/dc/terms/contributor",
+          "val" : "https://orcid.org/0000-0002-7356-1779"
+        } ]
+      }
     }, {
       "id" : "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym",
       "lbl" : "has_exact_synonym",
@@ -143,9 +150,6 @@
           "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label."
         },
         "basicPropertyValues" : [ {
-          "pred" : "http://purl.obolibrary.org/obo/IAO_0000117",
-          "val" : "http://orcid.org/0000-0001-5208-3432"
-        }, {
           "pred" : "http://purl.obolibrary.org/obo/IAO_0000233",
           "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20"
         }, {

mbao-simple.obo

@@ -1,13 +1,15 @@
 format-version: 1.2
-data-version: https://purl.brain-bican.org/ontology/mbao/releases/2023-08-25/mbao-simple.owl
+data-version: https://purl.brain-bican.org/ontology/mbao/releases/2025-02-10/mbao-simple.owl
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology ""
 subsetdef: http://purl.obolibrary.org/obo/valid_for_gocam ""
 ontology: https://purl.brain-bican.org/ontology/mbao/mbao-simple.owl
 property_value: dcterms-license http://creativecommons.org/licenses/by/4.0/
+property_value: has_ontology_root_term MBA:997
+property_value: http://purl.org/dc/terms/description "An application ontology built by combining ontologised versions of the Allen Institute Mouse Brain Atlas (MBA) StructureGraph mapped to Uberon." xsd:string
 property_value: http://purl.org/dc/terms/title "Mouse Brain Atlas Ontology" xsd:string
-property_value: owl:versionInfo "2023-08-25" xsd:string
+property_value: owl:versionInfo "2025-02-10" xsd:string
 
 [Typedef]
 id: dcterms-license
@@ -16,12 +18,17 @@ namespace: uberon
 xref: http://purl.org/dc/terms/license
 is_metadata_tag: true
 
+[Typedef]
+id: has_ontology_root_term
+name: has ontology root term
+namespace: uberon
+def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." []
+xref: IAO:0000700
+is_metadata_tag: true
+
 [Typedef]
 id: part_of
 name: part of
-name: part_of
-namespace: external
-namespace: quality
 namespace: spatial
 namespace: uberon
 def: "a core relation that holds between a part and its whole" []
@@ -30,22 +37,12 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term
 subset: http://purl.obolibrary.org/obo/valid_for_go_ontology
 subset: http://purl.obolibrary.org/obo/valid_for_gocam
 xref: BFO:0000050
-property_value: IAO:0000111 "is part of" xsd:string
 property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
 property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
 property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
 property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
 property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
 property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
-property_value: IAO:0000118 "part_of" xsd:string
-property_value: RO:0001900 RO:0001901
-property_value: RO:0040042 BFO:0000002
-property_value: RO:0040042 BFO:0000003
-property_value: RO:0040042 BFO:0000004
-property_value: RO:0040042 BFO:0000017
-property_value: RO:0040042 BFO:0000019
-property_value: RO:0040042 BFO:0000020
-property_value: RO:0040042 BFO:0000031
 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
 property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string