mappableConcept primaryCoding & iris (#110).

snapshot-2025-02.3 id updates

examples/mappable-concept-gene.yaml

@@ -1,20 +1,29 @@
-id: HGNC:1101
-primaryCode: BRCA2
-name: BRCA2 DNA repair associated
 conceptType: Gene
+name: BRCA2
+primaryCoding:
+  code: HGNC:1101
+  system: https://www.genenames.org/    
+  iris:
+  - https://identifiers.org/hgnc:1101
+  - https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/1101   
 mappings:
-- coding: 
-    code: HGNC:1101
-    system: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/
-  relation: exactMatch
 - coding: 
     code: ENSG00000139618
-    system: https://www.ensembl.org/id/
+    system: https://www.ensembl.org/
+    iris:
+      - https://identifiers.org/ensembl:ENSG00000139618
+      - https://www.ensembl.org/id/ENSG00000139618
+
   relation: closeMatch
 - coding: 
     code: "675"
     system: https://www.ncbi.nlm.nih.gov/gene/
+    iris:
+      - https://identifiers.org/ncbigene:675
+      - https://www.ncbi.nlm.nih.gov/gene/675
   relation: closeMatch
 extensions:
 - name: "AlsoKnownAs"
-  value: "FAD; FACD; FAD1; GLM3; BRCC2; FANCD; PNCA2; FANCD1; XRCC11; BROVCA2"
+  value: "FAD; FACD; FAD1; GLM3; BRCC2; FANCD; PNCA2; FANCD1; XRCC11; BROVCA2"
+- name: "description"
+  value: "BRCA2 DNA repair associated"

schema/gks-core/def/Coding.rst

@@ -43,7 +43,7 @@ Some Coding attributes are inherited from :ref:`Element`.
       - 
       - string
       - 1..1
-      - The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system. When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the Sequence Ontology).
+      - The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system.
    *  - systemVersion
       - 
       - string
@@ -53,4 +53,12 @@ Some Coding attributes are inherited from :ref:`Element`.
       - 
       - :ref:`code`
       - 1..1
-      - A symbol uniquely identifying the concept, as in a syntax defined by the code system. CURIE format is preferred where possible (e.g. 'SO:0000704' is the CURIE form of the Sequence Ontology code for 'gene').
+      - A symbol uniquely identifying the concept, as in a syntax defined by the code system. If a dereferencable identifier is available, it should be provided in the `iris` field.
+   *  - iris
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
+      - :ref:`iriReference`
+      - 0..m
+      - A list of IRIs that are associated with the coding. This can be used to provide additional context or to link to additional information about the concept.

schema/gks-core/def/MappableConcept.rst

@@ -4,22 +4,7 @@
 
 **Computational Definition**
 
-A concept name that may be mapped to one or more :ref:`Codings <Coding>`.
-
-**GA4GH Digest**
-
-.. list-table::
-    :class: clean-wrap
-    :header-rows: 1
-    :align: left
-    :widths: auto
-
-    *  - Prefix
-       - Inherent
-
-    *  - None
-       - ['primaryCode']
-
+A concept based on a primaryCoding and/or name that may be mapped to one or more other :ref:`Codings <Coding>`.
 
 **Information Model**
 
@@ -59,11 +44,11 @@ Some MappableConcept attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - A primary name for the concept.
-   *  - primaryCode
+   *  - primaryCoding
       - 
-      - :ref:`code`
+      - :ref:`Coding`
       - 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.
+      - A primary coding for the concept.
    *  - mappings
       - 
                         .. raw:: html

schema/gks-core/gks-core-source.yaml

@@ -1,5 +1,5 @@
 $schema: "https://json-schema.org/draft/2020-12/schema"
-$id: "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/gks-core-source.yaml"
+$id: "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/gks-core-source.yaml"
 title: GKS Core Class Definitions
 strict: true
 
@@ -117,11 +117,8 @@ $defs:
     inherits: Element
     type: object
     maturity: trial use
-    ga4gh:
-      inherent:
-        - primaryCode
     description: >-
-      A concept name that may be mapped to one or more :ref:`Codings <Coding>`.
+      A concept based on a primaryCoding and/or name that may be mapped to one or more other :ref:`Codings <Coding>`.
     properties:
       conceptType:
         type: string
@@ -134,14 +131,9 @@ $defs:
       name:
         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.
+      primaryCoding:
+        $ref: "#/$defs/Coding"
+        description: A primary coding for the concept.
       mappings:
         type: array
         ordered: false
@@ -154,7 +146,7 @@ $defs:
       - required:
           - name
       - required:
-          - primaryCode
+          - primaryCoding
 
   ConceptMapping:
     type: object
@@ -196,18 +188,22 @@ $defs:
         description: >-
           The terminology/code system that defined the code. May be reported as a free-text name
           (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system.
-          When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that
-          the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the
-          Sequence Ontology).
       systemVersion:
         type: string
         description: Version of the terminology or code system that provided the code.
       code:
         $ref: '#/$defs/code'
         description: >-
           A symbol uniquely identifying the concept, as in a syntax defined by the code system.
-          CURIE format is preferred where possible (e.g. 'SO:0000704' is the CURIE form of the
-          Sequence Ontology code for 'gene').
+          If a dereferencable identifier is available, it should be provided in the `iris` field.
+      iris:
+        type: array
+        ordered: false
+        items:
+          $ref: '#/$defs/iriReference'
+        description: >-
+          A list of IRIs that are associated with the coding. This can be used to provide additional
+          context or to link to additional information about the concept.
     required:
       - system
       - code

schema/gks-core/json/Code

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/code",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/code",
    "title": "code",
    "type": "string",
    "maturity": "trial use",

schema/gks-core/json/Coding

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Coding",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Coding",
    "title": "Coding",
    "type": "object",
    "maturity": "trial use",
@@ -14,7 +14,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
@@ -25,15 +25,23 @@
       },
       "system": {
          "type": "string",
-         "description": "The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system. When the 'code' is reported as a CURIE, the 'system' should be reported as the uri that the CURIE's prefix expands to (e.g. 'http://purl.obofoundry.org/so.owl/' for the Sequence Ontology)."
+         "description": "The terminology/code system that defined the code. May be reported as a free-text name (e.g. 'Sequence Ontology'), but it is preferable to provide a uri/url for the system."
       },
       "systemVersion": {
          "type": "string",
          "description": "Version of the terminology or code system that provided the code."
       },
       "code": {
-         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/code",
-         "description": "A symbol uniquely identifying the concept, as in a syntax defined by the code system. CURIE format is preferred where possible (e.g. 'SO:0000704' is the CURIE form of the Sequence Ontology code for 'gene')."
+         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/code",
+         "description": "A symbol uniquely identifying the concept, as in a syntax defined by the code system. If a dereferencable identifier is available, it should be provided in the `iris` field."
+      },
+      "iris": {
+         "type": "array",
+         "ordered": false,
+         "items": {
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/iriReference"
+         },
+         "description": "A list of IRIs that are associated with the coding. This can be used to provide additional context or to link to additional information about the concept."
       }
    },
    "required": [

schema/gks-core/json/ConceptMapping

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/ConceptMapping",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/ConceptMapping",
    "title": "ConceptMapping",
    "type": "object",
    "maturity": "trial use",
@@ -14,13 +14,13 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
       },
       "coding": {
-         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Coding",
+         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Coding",
          "description": "A structured representation of a code for a defined concept in a terminology or code system."
       },
       "relation": {

schema/gks-core/json/Extension

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Extension",
    "title": "Extension",
    "type": "object",
    "maturity": "trial use",
@@ -14,7 +14,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."

schema/gks-core/json/MappableConcept

@@ -1,15 +1,10 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/MappableConcept",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/MappableConcept",
    "title": "MappableConcept",
    "type": "object",
    "maturity": "trial use",
-   "ga4gh": {
-      "inherent": [
-         "primaryCode"
-      ]
-   },
-   "description": "A concept name that may be mapped to one or more Codings.",
+   "description": "A concept based on a primaryCoding and/or name that may be mapped to one or more other Codings.",
    "properties": {
       "id": {
          "type": "string",
@@ -19,7 +14,7 @@
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/Extension"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Extension"
          },
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
@@ -33,15 +28,15 @@
          "type": "string",
          "description": "A primary name for the concept."
       },
-      "primaryCode": {
-         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/code",
-         "description": "A primary code for the concept that is used to identify the concept in a terminology or code system. If there is a public code system for the primaryCode then it should also be specified in the mappings array with a relation of 'exactMatch'. This attribute is provided to both allow a more technical code to be used when a public Coding with a system is not available as well as when it is available but should be identified as the primary code."
+      "primaryCoding": {
+         "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/Coding",
+         "description": "A primary coding for the concept."
       },
       "mappings": {
          "type": "array",
          "ordered": false,
          "items": {
-            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/ConceptMapping"
+            "$ref": "/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/ConceptMapping"
          },
          "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
       }
@@ -54,7 +49,7 @@
       },
       {
          "required": [
-            "primaryCode"
+            "primaryCoding"
          ]
       }
    ],

schema/gks-core/json/date

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/date",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/date",
    "title": "date",
    "type": "string",
    "maturity": "trial use",

schema/gks-core/json/datetime

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/datetime",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/datetime",
    "title": "datetime",
    "type": "string",
    "maturity": "trial use",

schema/gks-core/json/iriReference

@@ -1,6 +1,6 @@
 {
    "$schema": "https://json-schema.org/draft/2020-12/schema",
-   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.2/json/iriReference",
+   "$id": "https://w3id.org/ga4gh/schema/gks-core/1.0.0-snapshot.2025-02.3/json/iriReference",
    "title": "iriReference",
    "type": "string",
    "maturity": "trial use",