add gks.common

ga4gh · Nov 28, 2023 · 762ebf7 · 762ebf7
1 parent a881d8d
commit 762ebf7
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Showing 26 changed files with 177 additions and 175 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "submodules/cat-vrs"]
+	path = submodules/cat-vrs
+	url = https://github.com/ga4gh/cat-vrs.git
diff --git a/schema/annotation-source.yaml b/schema/annotation-source.yaml
@@ -4,18 +4,16 @@ type: object
 strict: true
 
 imports:
-  gks.core: core-source.yaml
+  gks.common: gks.common-source.yaml
   vrs: vrs-source.yaml
-  catvars: catvars-source.yaml
 
 namespaces:
-  gks.core: core.json#/$defs/
-  catvars: catvars.json#/$defs/
+  gks.common: gks.common.json#/$defs/
   vrs: vrs.json#/$defs/
 
 $defs:
   InformationEntity:
-    inherits: gks.core:Entity
+    inherits: gks.common:Entity
     description: >-
       InformationEntities are abstract (non-physical) entities that are about something (i.e. they carry 
       information about things in the real world).
@@ -25,7 +23,7 @@ $defs:
       specifiedBy:
         oneOf:
         - $ref: "#/$defs/Method"
-        - $refCurie: gks.core:IRI
+        - $refCurie: gks.common:IRI
         description: >-
           A :ref:`Method` that describes all or part of the process through which the information was
           generated.
@@ -40,16 +38,16 @@ $defs:
         items:
           oneOf:
           - $ref: "#/$defs/Document"
-          - $refCurie: gks.core:IRI
+          - $refCurie: gks.common:IRI
         description: A document in which the information content is expressed.
       recordMetadata:
-        $refCurie: gks.core:RecordMetadata
+        $refCurie: gks.common:RecordMetadata
     heritableRequired:
       - id
       - type
   Contribution:
     type: object
-    inherits: gks.core:Entity
+    inherits: gks.common:Entity
     maturity: Alpha
     description: >-
       The sum of all actions taken by a single agent in contributing to the creation, modification, 
@@ -65,14 +63,14 @@ $defs:
         type: string
         format: date
       activity:
-        $refCurie: gks.core:Coding
+        $refCurie: gks.common:Coding
         description: >-
          SHOULD describe a concept descending from the Contributor Role Ontology.
 
   Agent:
     type: object
     maturity: Alpha
-    inherits: gks.core:Entity
+    inherits: gks.common:Entity
     description: >-
       An autonomous actor (person, organization, or computational agent) that bears some form
       of responsibility for an activity taking place, for the existence of an entity, or for 
@@ -94,7 +92,7 @@ $defs:
   Method:
     type: object
     maturity: Alpha
-    inherits: gks.core:Entity
+    inherits: gks.common:Entity
     description: >-
       A set of instructions that specify how to achieve some objective (e.g. experimental protocols, 
       curation guidelines, rule sets, etc.)
@@ -106,18 +104,18 @@ $defs:
         description: MUST be "Method".
       isReportedIn:
         oneOf:
-        - $refCurie: gks.core:IRI
+        - $refCurie: gks.common:IRI
         - $ref: "#/$defs/Document"
       subtype:
-        $refCurie: gks.core:Coding
+        $refCurie: gks.common:Coding
         description: >-
           A more specific type of entity the method represents (e.g. Variant Interpretation Guideline, 
           Experimental Protocol)
 
   Document:
     type: object
     maturity: Alpha
-    inherits: gks.core:MappableEntity
+    inherits: gks.common:MappableEntity
     description: a representation of a physical or digital document
     properties:
       type:
@@ -156,15 +154,15 @@ $defs:
         default: DataItem
         description: Must be "DataItem"
       subtype:
-        $refCurie: gks.core:Coding
+        $refCurie: gks.common:Coding
         description: >- 
           A specific type of data the DataItem object represents (e.g. a specimen count, a 
           patient weight, an allele frequency, a p-value, a confidence score)
       value:
          type: string
       unit:
         type:
-          $refCurie: gks.core:Coding
+          $refCurie: gks.common:Coding
     required: [ "value" ]
   Statement:
     inherits: InformationEntity
@@ -190,8 +188,8 @@ $defs:
           The direction of this Statement with respect to the predicate.
       strength:
         oneOf:
-          - $refCurie: gks.core:Coding
-          - $refCurie: gks.core:IRI
+          - $refCurie: gks.common:Coding
+          - $refCurie: gks.common:IRI
         description: >-
           The overall strength of support for the Statement based on all evidence assessed.
     heritableRequired:

diff --git a/schema/annotation.json b/schema/annotation.json
@@ -24,7 +24,7 @@
                "type": "array",
                "ordered": true,
                "items": {
-                  "$ref": "core.json#/$defs/Extension"
+                  "$ref": "gks.common.json#/$defs/Extension"
                }
             },
             "type": {
@@ -40,7 +40,7 @@
             },
             "activity": {
                "description": "SHOULD describe a concept descending from the Contributor Role Ontology.",
-               "$ref": "core.json#/$defs/Coding"
+               "$ref": "gks.common.json#/$defs/Coding"
             }
          },
          "required": [],
@@ -67,7 +67,7 @@
                "type": "array",
                "ordered": true,
                "items": {
-                  "$ref": "core.json#/$defs/Extension"
+                  "$ref": "gks.common.json#/$defs/Extension"
                }
             },
             "type": {
@@ -112,7 +112,7 @@
                "type": "array",
                "ordered": true,
                "items": {
-                  "$ref": "core.json#/$defs/Extension"
+                  "$ref": "gks.common.json#/$defs/Extension"
                }
             },
             "type": {
@@ -127,13 +127,13 @@
                      "$ref": "#/$defs/Document"
                   },
                   {
-                     "$ref": "core.json#/$defs/IRI"
+                     "$ref": "gks.common.json#/$defs/IRI"
                   }
                ]
             },
             "subtype": {
                "description": "A more specific type of entity the method represents (e.g. Variant Interpretation Guideline,  Experimental Protocol)",
-               "$ref": "core.json#/$defs/Coding"
+               "$ref": "gks.common.json#/$defs/Coding"
             }
          },
          "required": [],
@@ -160,14 +160,14 @@
                "type": "array",
                "ordered": true,
                "items": {
-                  "$ref": "core.json#/$defs/Extension"
+                  "$ref": "gks.common.json#/$defs/Extension"
                }
             },
             "mappings": {
                "type": "array",
                "ordered": false,
                "items": {
-                  "$ref": "core.json#/$defs/Mapping"
+                  "$ref": "gks.common.json#/$defs/Mapping"
                }
             },
             "type": {
@@ -220,7 +220,7 @@
                "type": "array",
                "ordered": true,
                "items": {
-                  "$ref": "core.json#/$defs/Extension"
+                  "$ref": "gks.common.json#/$defs/Extension"
                }
             },
             "type": {
@@ -235,7 +235,7 @@
                      "$ref": "#/$defs/Method"
                   },
                   {
-                     "$ref": "core.json#/$defs/IRI"
+                     "$ref": "gks.common.json#/$defs/IRI"
                   }
                ],
                "description": "A Method that describes all or part of the process through which the information was generated."
@@ -256,25 +256,25 @@
                         "$ref": "#/$defs/Document"
                      },
                      {
-                        "$ref": "core.json#/$defs/IRI"
+                        "$ref": "gks.common.json#/$defs/IRI"
                      }
                   ]
                },
                "description": "A document in which the information content is expressed."
             },
             "recordMetadata": {
-               "$ref": "core.json#/$defs/RecordMetadata"
+               "$ref": "gks.common.json#/$defs/RecordMetadata"
             },
             "subtype": {
                "description": "A specific type of data the DataItem object represents (e.g. a specimen count, a  patient weight, an allele frequency, a p-value, a confidence score)",
-               "$ref": "core.json#/$defs/Coding"
+               "$ref": "gks.common.json#/$defs/Coding"
             },
             "value": {
                "type": "string"
             },
             "unit": {
                "type": {
-                  "$ref": "core.json#/$defs/Coding"
+                  "$ref": "gks.common.json#/$defs/Coding"
                }
             }
          },

diff --git a/schema/annotation.yaml b/schema/annotation.yaml
@@ -25,7 +25,7 @@ $defs:
         type: array
         ordered: true
         items:
-          $ref: core.json#/$defs/Extension
+          $ref: gks.common.json#/$defs/Extension
       type:
         type: string
         const: Contribution
@@ -37,7 +37,7 @@ $defs:
       activity:
         description: SHOULD describe a concept descending from the Contributor Role
           Ontology.
-        $ref: core.json#/$defs/Coding
+        $ref: gks.common.json#/$defs/Coding
     required: []
     additionalProperties: false
   Agent:
@@ -63,7 +63,7 @@ $defs:
         type: array
         ordered: true
         items:
-          $ref: core.json#/$defs/Extension
+          $ref: gks.common.json#/$defs/Extension
       type:
         type: string
         const: Agent
@@ -101,7 +101,7 @@ $defs:
         type: array
         ordered: true
         items:
-          $ref: core.json#/$defs/Extension
+          $ref: gks.common.json#/$defs/Extension
       type:
         type: string
         const: Method
@@ -110,11 +110,11 @@ $defs:
       isReportedIn:
         oneOf:
         - $ref: '#/$defs/Document'
-        - $ref: core.json#/$defs/IRI
+        - $ref: gks.common.json#/$defs/IRI
       subtype:
         description: A more specific type of entity the method represents (e.g. Variant
           Interpretation Guideline,  Experimental Protocol)
-        $ref: core.json#/$defs/Coding
+        $ref: gks.common.json#/$defs/Coding
     required: []
     additionalProperties: false
   Document:
@@ -138,12 +138,12 @@ $defs:
         type: array
         ordered: true
         items:
-          $ref: core.json#/$defs/Extension
+          $ref: gks.common.json#/$defs/Extension
       mappings:
         type: array
         ordered: false
         items:
-          $ref: core.json#/$defs/Mapping
+          $ref: gks.common.json#/$defs/Mapping
       type:
         type: string
         const: Document
@@ -189,7 +189,7 @@ $defs:
         type: array
         ordered: true
         items:
-          $ref: core.json#/$defs/Extension
+          $ref: gks.common.json#/$defs/Extension
       type:
         type: string
         const: DataItem
@@ -198,7 +198,7 @@ $defs:
       specifiedBy:
         oneOf:
         - $ref: '#/$defs/Method'
-        - $ref: core.json#/$defs/IRI
+        - $ref: gks.common.json#/$defs/IRI
         description: A Method that describes all or part of the process through which
           the information was generated.
       contributions:
@@ -212,20 +212,20 @@ $defs:
         items:
           oneOf:
           - $ref: '#/$defs/Document'
-          - $ref: core.json#/$defs/IRI
+          - $ref: gks.common.json#/$defs/IRI
         description: A document in which the information content is expressed.
       recordMetadata:
-        $ref: core.json#/$defs/RecordMetadata
+        $ref: gks.common.json#/$defs/RecordMetadata
       subtype:
         description: A specific type of data the DataItem object represents (e.g.
           a specimen count, a  patient weight, an allele frequency, a p-value, a confidence
           score)
-        $ref: core.json#/$defs/Coding
+        $ref: gks.common.json#/$defs/Coding
       value:
         type: string
       unit:
         type:
-          $ref: core.json#/$defs/Coding
+          $ref: gks.common.json#/$defs/Coding
     required:
     - id
     - type

diff --git a/schema/catvars-source.yaml b/schema/catvars-source.yaml
diff --git a/schema/catvars.json b/schema/catvars.json
diff --git a/schema/catvrs-source.yaml b/schema/catvrs-source.yaml
@@ -0,0 +1 @@
+../submodules/cat-vrs/schema/catvrs-source.yaml
diff --git a/schema/catvrs.json b/schema/catvrs.json
@@ -0,0 +1 @@
+../submodules/cat-vrs/schema/catvrs.json
diff --git a/schema/core-source.yaml b/schema/core-source.yaml
diff --git a/schema/core.json b/schema/core.json
diff --git a/schema/defs/annotation/Agent.rst b/schema/defs/annotation/Agent.rst
@@ -4,7 +4,7 @@ An autonomous actor (person, organization, or computational agent) that bears so
 
     **Information Model**
 
-Some Agent attributes are inherited from :ref:`gks.core:Entity`.
+Some Agent attributes are inherited from :ref:`gks.common:Entity`.
 
     .. list-table::
        :class: clean-wrap
@@ -29,7 +29,7 @@ Some Agent attributes are inherited from :ref:`gks.core:Entity`.
           - 0..1
           - A free-text description of the entity.
        *  - extensions
-          - `Extension <core.json#/$defs/Extension>`_
+          - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
        *  - type