Merge pull request #249 from alliance-genome/interaction_updates

Interaction IDs
alliance-genome · Mar 15, 2024 · 11f5bb8 · 11f5bb8
2 parents 6f6e60b + 6ff8aa8
commit 11f5bb8
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Showing 3 changed files with 39 additions and 23 deletions.
diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json
@@ -12550,10 +12550,6 @@
                     },
                     "type": "array"
                 },
-                "curie": {
-                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
-                    "type": "string"
-                },
                 "date_created": {
                     "description": "The date on which an entity was created. This can be applied to nodes or edges.",
                     "format": "date-time",
@@ -12589,6 +12585,10 @@
                     "$ref": "#/$defs/Gene",
                     "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa."
                 },
+                "interaction_id": {
+                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
+                    "type": "string"
+                },
                 "interaction_source": {
                     "description": "The interaction database that curated the interaction. e.g. BioGRID An MITerm from the AGR interaction source subset of AGR terms.",
                     "type": "string"
@@ -12643,6 +12643,10 @@
                     "description": "A high-level grouping for the relationship type. This is analogous to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type.",
                     "type": "string"
                 },
+                "unique_id": {
+                    "description": "A non-curie unique identifier for a thing.",
+                    "type": "string"
+                },
                 "updated_by": {
                     "description": "The individual that last modified the entity.",
                     "type": "string"
@@ -12675,10 +12679,6 @@
                     },
                     "type": "array"
                 },
-                "curie": {
-                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
-                    "type": "string"
-                },
                 "date_created": {
                     "description": "The date on which an entity was created. This can be applied to nodes or edges.",
                     "format": "date-time",
@@ -12710,6 +12710,10 @@
                     "description": "Name of VocabularyTerm describing relationship between a subject entity and an object Gene",
                     "type": "string"
                 },
+                "interaction_id": {
+                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
+                    "type": "string"
+                },
                 "interaction_source_curie": {
                     "description": "The interaction database that curated the interaction. e.g. BioGRID. Value is the curie of an MITerm from the AGR interaction source subset of AGR terms.",
                     "type": "string"
@@ -12971,10 +12975,6 @@
                     },
                     "type": "array"
                 },
-                "curie": {
-                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
-                    "type": "string"
-                },
                 "date_created": {
                     "description": "The date on which an entity was created. This can be applied to nodes or edges.",
                     "format": "date-time",
@@ -13014,6 +13014,10 @@
                     "$ref": "#/$defs/Gene",
                     "description": "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa."
                 },
+                "interaction_id": {
+                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
+                    "type": "string"
+                },
                 "interaction_source": {
                     "description": "The interaction database that curated the interaction. e.g. BioGRID An MITerm from the AGR interaction source subset of AGR terms.",
                     "type": "string"
@@ -13056,6 +13060,10 @@
                     "description": "A high-level grouping for the relationship type. This is analogous to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type.",
                     "type": "string"
                 },
+                "unique_id": {
+                    "description": "A non-curie unique identifier for a thing.",
+                    "type": "string"
+                },
                 "updated_by": {
                     "description": "The individual that last modified the entity.",
                     "type": "string"
@@ -13092,10 +13100,6 @@
                     },
                     "type": "array"
                 },
-                "curie": {
-                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
-                    "type": "string"
-                },
                 "date_created": {
                     "description": "The date on which an entity was created. This can be applied to nodes or edges.",
                     "format": "date-time",
@@ -13131,6 +13135,10 @@
                     "description": "Name of VocabularyTerm describing relationship between a subject entity and an object Gene",
                     "type": "string"
                 },
+                "interaction_id": {
+                    "description": "The unique primary identifier for the interaction. This should be the source (curation) database identifier, or if that is not available then the aggregation database identifier (e.g. IMEx)",
+                    "type": "string"
+                },
                 "interaction_source_curie": {
                     "description": "The interaction database that curated the interaction. e.g. BioGRID. Value is the curie of an MITerm from the AGR interaction source subset of AGR terms.",
                     "type": "string"

diff --git a/model/schema/geneInteraction.yaml b/model/schema/geneInteraction.yaml
@@ -91,7 +91,8 @@ classes:
     is_a: GeneGeneAssociation
     abstract: true
     slots:
-      - curie
+      - unique_id
+      - interaction_id
       - cross_references
       - interaction_source
       - interaction_type
@@ -116,7 +117,7 @@ classes:
       - WB
       - WWPDB
     slot_usage:
-      curie:
+      interaction_id:
         description: >-
           The unique primary identifier for the interaction. This should be the source
           (curation) database identifier, or if that is not available then the aggregation
@@ -138,7 +139,7 @@ classes:
       molecular interaction between gene products (e.g. protein-protein interactions),
       or may be a genetic interaction between genes (e.g. phenotypic suppression)
     slots:
-      - curie
+      - interaction_id
       - cross_reference_dtos
       - interaction_source_curie
       - interaction_type_curie
@@ -147,7 +148,7 @@ classes:
       - interactor_A_type_curie
       - interactor_B_type_curie
     slot_usage:
-      curie:
+      interaction_id:
         description: >-
           The unique primary identifier for the interaction. This should be the source
           (curation) database identifier, or if that is not available then the aggregation
@@ -247,6 +248,13 @@ slots:
     range: string
     required: true
 
+  interaction_id:
+    description: >-
+      Identifier for interaction provided by MOD or other external source
+    domain: GeneInteraction
+    range: string
+    required: false
+
   interaction_source:
     range: MITerm
     description: >-

diff --git a/test/data/gene_interaction_test.json b/test/data/gene_interaction_test.json
@@ -2,7 +2,7 @@
     "linkml_version": "2.0.0",
     "gene_genetic_interaction_ingest_set": [
         {
-            "curie": "WB:WBCnstr00000001",
+            "interaction_id": "WB:WBInteraction000524000",
             "subject_gene_identifier": "WB:WBGene00000001",
             "object_gene_identifier": "WB:WBGene00000002",
             "gene_relation_name": "interacts_with",
@@ -30,7 +30,7 @@
     ],
     "gene_molecular_interaction_ingest_set": [
         {
-            "curie": "WB:WBCnstr00000002",
+            "interaction_id": "WB:WBInteraction000123456",
             "subject_gene_identifier": "WB:WBGene00000003",
             "object_gene_identifier": "WB:WBGene00000004",
             "gene_relation_name": "physically_interacts_with",
@@ -53,4 +53,4 @@
             "detection_method_curie": "MI:0364"
         }
     ]
-}
+}