1.x merge 1.0.0 snapshot work (#109)

* MappableConcept inherent properties * Updates to Coding in gks-core-source.yaml * renamed label/altLabels to name/aliases as discussed with AW/MB.
ga4gh · Feb 10, 2025 · a4b4f81 · a4b4f81
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diff --git a/examples/mappable-concept-gene.yaml b/examples/mappable-concept-gene.yaml
@@ -1,6 +1,6 @@
 id: HGNC:1101
 primaryCode: BRCA2
-label: BRCA2 DNA repair associated
+name: BRCA2 DNA repair associated
 conceptType: Gene
 mappings:
 - coding: 

diff --git a/examples/simple-coding.yaml b/examples/simple-coding.yaml
@@ -1,4 +1,4 @@
-label: foo
+name: foo
 system: https://bar.com
 systemVersion: "2"
 code: "SCV213.1"
diff --git a/schema/gks-core/def/Coding.rst b/schema/gks-core/def/Coding.rst
@@ -1,5 +1,5 @@
-.. note:: This data class is at a **trial use** maturity level and may \
-    change in future releases. Maturity \
+.. warning:: This data class is at a **draft** maturity level and may \
+    change significantly in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**
@@ -34,7 +34,7 @@ Some Coding attributes are inherited from :ref:`Element`.
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
-   *  - label
+   *  - name
       - 
       - string
       - 0..1

diff --git a/schema/gks-core/def/ConceptMapping.rst b/schema/gks-core/def/ConceptMapping.rst
@@ -1,5 +1,5 @@
-.. note:: This data class is at a **trial use** maturity level and may \
-    change in future releases. Maturity \
+.. warning:: This data class is at a **draft** maturity level and may \
+    change significantly in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**

diff --git a/schema/gks-core/def/Entity.rst b/schema/gks-core/def/Entity.rst
@@ -30,7 +30,7 @@ Anything that exists, has existed, or will exist.
       - string
       - 1..1
       - The name of the class that is instantiated by a data object representing the Entity.
-   *  - label
+   *  - name
       - 
       - string
       - 0..1
@@ -40,7 +40,7 @@ Anything that exists, has existed, or will exist.
       - string
       - 0..1
       - A free-text description of the Entity.
-   *  - alternativeLabels
+   *  - aliases
       - 
                         .. raw:: html
 

diff --git a/schema/gks-core/def/MappableConcept.rst b/schema/gks-core/def/MappableConcept.rst
@@ -1,10 +1,10 @@
-.. note:: This data class is at a **trial use** maturity level and may \
-    change in future releases. Maturity \
+.. warning:: This data class is at a **draft** maturity level and may \
+    change significantly in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**
 
-A concept label that may be mapped to one or more :ref:`Codings <Coding>`.
+A concept name that may be mapped to one or more :ref:`Codings <Coding>`.
 
 **Information Model**
 
@@ -39,7 +39,7 @@ Some MappableConcept attributes are inherited from :ref:`Element`.
       - string
       - 0..1
       - A term indicating the type of concept being represented by the MappableConcept.
-   *  - label
+   *  - name
       - 
       - string
       - 0..1

diff --git a/schema/gks-core/gks-core-source.yaml b/schema/gks-core/gks-core-source.yaml
@@ -10,7 +10,7 @@ $defs:
     description: Anything that exists, has existed, or will exist.
     $comment: >-
       Entity is the root class of the 'gks-core' information model. All core classes that
-      have ids and other general metadata like label, description, type, or extensions descend from
+      have ids and other general metadata like name, description, type, or extensions descend from
       this class and inherit its attributes.
     heritableProperties:
       id:
@@ -30,14 +30,14 @@ $defs:
         type: string
         description: >-
           The name of the class that is instantiated by a data object representing the Entity.
-        $comment: MUST be the label of a concrete class from the data model.
-      label:
+        $comment: MUST be the name of a concrete class from the data model.
+      name:
         type: string
         description: A primary name for the entity.
       description:
         type: string
         description: A free-text description of the Entity.
-      alternativeLabels:
+      aliases:
         type: array
         ordered: false
         items:
@@ -116,12 +116,12 @@ $defs:
   MappableConcept:
     inherits: Element
     type: object
-    maturity: trial use
+    maturity: draft
     ga4gh:
       inherent:
         - primaryCode
     description: >-
-      A concept label that may be mapped to one or more :ref:`Codings <Coding>`.
+      A concept name that may be mapped to one or more :ref:`Codings <Coding>`.
     properties:
       conceptType:
         type: string
@@ -131,7 +131,7 @@ $defs:
           This attribute can be used to indicate the type of concept being represented by the MappableConcept.
           For example, in a variant pathogenicity assessment, the conceptType could be 'Pathogenicity Strength',
           'Disease', 'Phenotype', 'Drug', 'Tumor Type', 'Evidence Direction', 'Evidence Strength', etc.
-      label:
+      name:
         type: string
         description: A primary name for the concept.
       primaryCode:
@@ -152,14 +152,14 @@ $defs:
           include a coding and a relation.
     anyOf:
       - required:
-          - label
+          - name
       - required:
           - primaryCode
 
   ConceptMapping:
     type: object
     inherits: Element
-    maturity: trial use
+    maturity: draft
     description: >-
       A mapping to a concept in a terminology or code system.
     properties:
@@ -184,11 +184,11 @@ $defs:
   Coding:
     inherits: Element
     type: object
-    maturity: trial use
+    maturity: draft
     description: >-
       A structured representation of a code for a defined concept in a terminology or code system.
     properties:
-      label:
+      name:
         type: string
         description: The human-readable name for the coded concept, as defined by the code system.
       system:

diff --git a/schema/gks-core/json/Coding b/schema/gks-core/json/Coding
@@ -3,7 +3,7 @@
    "$id": "https://w3id.org/ga4gh/schema/gks-core/1.x/json/Coding",
    "title": "Coding",
    "type": "object",
-   "maturity": "trial use",
+   "maturity": "draft",
    "description": "A structured representation of a code for a defined concept in a terminology or code system.",
    "properties": {
       "id": {
@@ -19,7 +19,7 @@
          "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
          "$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."
       },
-      "label": {
+      "name": {
          "type": "string",
          "description": "The human-readable name for the coded concept, as defined by the code system."
       },

diff --git a/schema/gks-core/json/ConceptMapping b/schema/gks-core/json/ConceptMapping
@@ -3,7 +3,7 @@
    "$id": "https://w3id.org/ga4gh/schema/gks-core/1.x/json/ConceptMapping",
    "title": "ConceptMapping",
    "type": "object",
-   "maturity": "trial use",
+   "maturity": "draft",
    "description": "A mapping to a concept in a terminology or code system.",
    "properties": {
       "id": {

diff --git a/schema/gks-core/json/MappableConcept b/schema/gks-core/json/MappableConcept
@@ -3,13 +3,13 @@
    "$id": "https://w3id.org/ga4gh/schema/gks-core/1.x/json/MappableConcept",
    "title": "MappableConcept",
    "type": "object",
-   "maturity": "trial use",
+   "maturity": "draft",
    "ga4gh": {
       "inherent": [
          "primaryCode"
       ]
    },
-   "description": "A concept label that may be mapped to one or more Codings.",
+   "description": "A concept name that may be mapped to one or more Codings.",
    "properties": {
       "id": {
          "type": "string",
@@ -29,7 +29,7 @@
          "description": "A term indicating the type of concept being represented by the MappableConcept.",
          "$comment": "This attribute can be used to indicate the type of concept being represented by the MappableConcept. For example, in a variant pathogenicity assessment, the conceptType could be 'Pathogenicity Strength', 'Disease', 'Phenotype', 'Drug', 'Tumor Type', 'Evidence Direction', 'Evidence Strength', etc."
       },
-      "label": {
+      "name": {
          "type": "string",
          "description": "A primary name for the concept."
       },
@@ -49,7 +49,7 @@
    "anyOf": [
       {
          "required": [
-            "label"
+            "name"
          ]
       },
       {