Merge pull request #270 from alliance-genome/SCRUM-4190

Scrum 4190
alliance-genome · Oct 24, 2024 · 7e4ca7c · 7e4ca7c
2 parents 7ca56f9 + 7f46c39
commit 7e4ca7c
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diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json
@@ -14395,6 +14395,81 @@
             "title": "GeneNomenclatureSet",
             "type": "object"
         },
+        "GeneOntologyAnnotation": {
+            "additionalProperties": false,
+            "description": "An annotation associating a gene to a Gene Ontology (GO) term",
+            "properties": {
+                "created_by": {
+                    "description": "The individual that created the entity.",
+                    "type": "string"
+                },
+                "date_created": {
+                    "description": "The date on which an entity was created. This can be applied to nodes or edges.",
+                    "format": "date-time",
+                    "type": "string"
+                },
+                "date_updated": {
+                    "description": "Date on which an entity was last modified.",
+                    "format": "date-time",
+                    "type": "string"
+                },
+                "db_date_created": {
+                    "description": "The date on which an entity was created in the Alliance database.  This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).",
+                    "format": "date-time",
+                    "type": "string"
+                },
+                "db_date_updated": {
+                    "description": "Date on which an entity was last modified in the Alliance database.  This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.",
+                    "format": "date-time",
+                    "type": "string"
+                },
+                "go_term": {
+                    "description": "the Gene Ontology (GO) term to which the gene is being annotated",
+                    "type": "string"
+                },
+                "internal": {
+                    "description": "Classifies the entity as private (for internal use) or not (for public use).",
+                    "type": "boolean"
+                },
+                "obsolete": {
+                    "description": "Entity is no longer current.",
+                    "type": "boolean"
+                },
+                "single_gene": {
+                    "$ref": "#/$defs/Gene"
+                },
+                "updated_by": {
+                    "description": "The individual that last modified the entity.",
+                    "type": "string"
+                }
+            },
+            "required": [
+                "go_term",
+                "internal"
+            ],
+            "title": "GeneOntologyAnnotation",
+            "type": "object"
+        },
+        "GeneOntologyAnnotationDTO": {
+            "additionalProperties": false,
+            "description": "An annotation associating a gene to a Gene Ontology (GO) term (DTO class)",
+            "properties": {
+                "gene_identifier": {
+                    "description": "Identifier (curie/primary_external_id/mod_internal_id) of the gene",
+                    "type": "string"
+                },
+                "go_term_curie": {
+                    "description": "the Gene Ontology (GO) term to which the gene is being annotated",
+                    "type": "string"
+                }
+            },
+            "required": [
+                "gene_identifier",
+                "go_term_curie"
+            ],
+            "title": "GeneOntologyAnnotationDTO",
+            "type": "object"
+        },
         "GenePathwayAssociation": {
             "additionalProperties": false,
             "description": "",

diff --git a/model/schema/gene.yaml b/model/schema/gene.yaml
@@ -204,6 +204,27 @@ classes:
           These notes should capture the reason for the event (e.g., rename or
           merge).
 
+  GeneOntologyAnnotation:
+    is_a: AuditedObject
+    description: An annotation associating a gene to a Gene Ontology (GO) term
+    slots:
+      - single_gene
+      - go_term
+    slot_usage:
+      go_term:
+        required: true
+
+  GeneOntologyAnnotationDTO:
+    description: An annotation associating a gene to a Gene Ontology (GO) term (DTO class)
+    slots:
+      - gene_identifier
+      - go_term_curie
+    slot_usage:
+      gene_identifier:
+        required: true
+      go_term_curie:
+        required: true
+
   GeneGenomicLocationAssociation:
     is_a: LocationAssociation
     description: >-
@@ -286,6 +307,16 @@ slots:
     required: true
     range: Gene
 
+  go_term:
+    description: the Gene Ontology (GO) term to which the gene is being annotated
+    range: GOTerm
+    multivalued: false
+
+  go_term_curie:
+    description: the Gene Ontology (GO) term to which the gene is being annotated
+    range: string
+    multivalued: false
+
   left_boundary_marker:
     description: >-
       The left boundary of a feature location relative to the landmark's