Add pathogenicityPredictions and allele to frequency

ga4gh-beacon · Jun 15, 2023 · b7a0060 · b7a0060
1 parent e7d7962
commit b7a0060
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diff --git a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
@@ -441,6 +441,13 @@
         },
         "PopulationFrequency": {
             "properties": {
+                "allele": {
+                    "description": "Specific allele associated with the frequency.",
+                    "examples": [
+                        "A"
+                    ],
+                    "type": "string"
+                },
                 "alleleFrequency": {
                     "description": "Allele frequency between 0 and 1.",
                     "examples": [
@@ -512,6 +519,12 @@
                     },
                     "type": "array"
                 },
+                "pathogenicityPredictions": {
+                    "items": {
+                        "$ref": "#/definitions/PhenoClinicEffect"
+                    },
+                    "type": "array"
+                },
                 "phenotypicEffects": {
                     "items": {
                         "$ref": "#/definitions/PhenoClinicEffect"

diff --git a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
@@ -321,6 +321,11 @@ definitions:
         description: Allele frequency between 0 and 1.
         examples:
           - 3.186e-05
+      allele:
+        type: string
+        description: Specific allele associated with the frequency.
+        examples:
+          - A
     required:
       - population
       - alleleFrequency
@@ -412,6 +417,10 @@ definitions:
         type: array
         items:
           $ref: '#/definitions/PhenoClinicEffect'
+      pathogenicityPredictions:
+        type: array
+        items:
+          $ref: '#/definitions/PhenoClinicEffect'
   SoftwareTool:
     type: object
     properties: