Add primaryCode to MappableConcept (#98)

ga4gh · Nov 15, 2024 · 0f315ae · 0f315ae
1 parent 9831bdc
commit 0f315ae
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diff --git a/examples/mappable-concept-gene.yaml b/examples/mappable-concept-gene.yaml
@@ -1,5 +1,7 @@
 id: HGNC:1101
-label: BRCA2
+primaryCode: BRCA2
+label: BRCA2 DNA repair associated
+conceptType: Gene
 mappings:
 - coding: 
     code: HGNC:1101

diff --git a/schema/gks-core/def/MappableConcept.rst b/schema/gks-core/def/MappableConcept.rst
@@ -44,6 +44,11 @@ Some MappableConcept attributes are inherited from :ref:`Element`.
       - string
       - 1..1
       - A primary name for the concept.
+   *  - primaryCode
+      - 
+      - :ref:`code`
+      - 0..1
+      - A primary code for the concept that is used to identify the concept in a terminology or code system. If there is a public code system for the primaryCode then it should also be specified in the mappings array with a relation of 'exactMatch'. This attribute is provided to both allow a more technical code to be used when a public Coding with a system is not available as well as when it is available but should be identified as the primary code.
    *  - mappings
       - 
                         .. raw:: html

diff --git a/schema/gks-core/gks-core-source.yaml b/schema/gks-core/gks-core-source.yaml
@@ -131,6 +131,14 @@ $defs:
       label:
         type: string
         description: A primary name for the concept.
+      primaryCode:
+        $ref: "#/$defs/code"
+        description: >-
+          A primary code for the concept that is used to identify the concept in a terminology or code system.
+          If there is a public code system for the primaryCode then it should also be specified in the mappings
+          array with a relation of 'exactMatch'. This attribute is provided to both allow a more technical code
+          to be used when a public Coding with a system is not available as well as when it is available but
+          should be identified as the primary code.
       mappings:
         type: array
         ordered: false

diff --git a/schema/gks-core/json/MappableConcept b/schema/gks-core/json/MappableConcept
@@ -28,6 +28,10 @@
          "type": "string",
          "description": "A primary name for the concept."
       },
+      "primaryCode": {
+         "$ref": "/ga4gh/schema/gks-core/1.x/json/code",
+         "description": "A primary code for the concept that is used to identify the concept in a terminology or code system. If there is a public code system for the primaryCode then it should also be specified in the mappings array with a relation of 'exactMatch'. This attribute is provided to both allow a more technical code to be used when a public Coding with a system is not available as well as when it is available but should be identified as the primary code."
+      },
       "mappings": {
          "type": "array",
          "ordered": false,