Merge pull request #278 from alliance-genome/Add-synonyms-slot-to-Var…

…iant-and-VariantDTO Add synonyms slot to Variant and VariantDTO
alliance-genome · Dec 17, 2024 · 6a0e13c · 6a0e13c
2 parents 6118279 + 21d6be5
commit 6a0e13c
Show file tree

Hide file tree

Showing 4 changed files with 19 additions and 0 deletions.
diff --git a/generated/jsonschema/allianceModel.schema.json b/generated/jsonschema/allianceModel.schema.json
@@ -24744,6 +24744,13 @@
                     },
                     "type": "array"
                 },
+                "synonyms": {
+                    "description": "A generic free-text field for objects that only have string representation of one or more synonyms and do not require meta data or attribution; if meta data or attribution are required to be captured for individual synonyms, consider the NameSlotAnnotation class",
+                    "items": {
+                        "type": "string"
+                    },
+                    "type": "array"
+                },
                 "taxon": {
                     "description": "The taxon from which the biological entity derives.",
                     "type": "string"
@@ -24836,6 +24843,13 @@
                     },
                     "type": "array"
                 },
+                "synonyms": {
+                    "description": "A generic free-text field for objects that only have string representation of one or more synonyms and do not require meta data or attribution; if meta data or attribution are required to be captured for individual synonyms, consider the NameSlotAnnotation class",
+                    "items": {
+                        "type": "string"
+                    },
+                    "type": "array"
+                },
                 "taxon_curie": {
                     "description": "Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives",
                     "type": "string"

diff --git a/model/schema/variantDTO.yaml b/model/schema/variantDTO.yaml
@@ -43,6 +43,7 @@ classes:
     slots:
       - variant_type_curie
       - note_dtos
+      - synonyms
       - source_general_consequence_dtos
       - variant_status_name
 

diff --git a/model/schema/variation.yaml b/model/schema/variation.yaml
@@ -51,6 +51,7 @@ classes:
     slots:
       - variant_type
       - related_notes
+      - synonyms
       - source_general_consequences
       - curated_variant_genomic_locations
       - curated_variant_transcript_locations

diff --git a/test/data/variant_test.json b/test/data/variant_test.json
@@ -3,6 +3,9 @@
   "variant_ingest_set": [
     {
       "primary_external_id": "ZFIN:ZDB-ALT-000412-8",
+      "synonyms": [
+        "name: I:g.118901G>A"
+      ],
       "data_provider_dto": {
         "source_organization_abbreviation": "ZFIN",
         "cross_reference_dto": {