added connect label to schema id

ga4gh · Sep 5, 2024 · e6a29f7 · e6a29f7
1 parent cf476d6
commit e6a29f7
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Showing 16 changed files with 79 additions and 91 deletions.
diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml
@@ -1,5 +1,5 @@
 $schema: "https://json-schema.org/draft/2020-12/schema"
-$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/cat-vrs-source.yaml"
+$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09/cat-vrs-source.yaml"
 title: GA4GH-Cat-VRS-Definitions
 type: object
 strict: true
@@ -37,7 +37,7 @@ $defs:
           this categorical variant.
         items:
           oneOf:
-            - $ref: "/ga4gh/schema/vrs/2.x/json/Variation"
+            - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation"
             - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
 
   ProteinSequenceConsequence:
@@ -58,7 +58,7 @@ $defs:
         description: 'MUST be "ProteinSequenceConsequence"'
       definingContext:
         oneOf:
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Allele"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele"
           - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
         description: >-
           The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
@@ -84,7 +84,7 @@ $defs:
         description: 'MUST be "CanonicalAllele"'
       definingContext:
         oneOf:
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Allele"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele"
           - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
         description: >-
           The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
@@ -111,10 +111,10 @@ $defs:
         description: 'MUST be "CategoricalCnv"'
       location:
         oneOf:
-          - $ref: "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/SequenceLocation"
           - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
         description: >-
-          A `VRS Location <https://vrs.ga4gh.org/en/2.x/concepts/location/SequenceLocation.html>`_
+          A `VRS Location <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08.1/concepts/location/SequenceLocation.html>`_
           object that represents a sequence derived from that location, and is congruent with locations 
           on alternate reference sequences.
       locationMatchCharacteristic:
@@ -138,7 +138,7 @@ $defs:
       copies:
         oneOf:
           - type: integer
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
         description: >-
           The integral number of copies of the subject in a system.
     required:
@@ -239,7 +239,7 @@ $defs:
       count:
         oneOf:
           - type: integer
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
         description: >-
           The integral quantity or quantity range of the subject in a system
     required: [ "count" ]
@@ -265,7 +265,7 @@ $defs:
       change:
         oneOf:
           - type: integer
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
           - copyChange:
             type: string
             enum: [ "EFO:0030069", "EFO:0020073", "EFO:0030068", "EFO:0030067", "EFO:0030064", "EFO:0030070",
@@ -322,7 +322,7 @@ $defs:
   #     copies:
   #       oneOf:
   #         - type: integer
-  #         - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+  #         - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
   #       description: >-
   #         The integral number of copies of the subject in a system.
   #   required:

diff --git a/schema/cat-vrs/def/CanonicalAllele.rst b/schema/cat-vrs/def/CanonicalAllele.rst
@@ -19,36 +19,36 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
    *  - id
       - string
       - 0..1
-      - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+      - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
    *  - label
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
       - string
       - 0..1
-      - A free-text description of the Entity.
+      - A free-text description of the entity.
    *  - alternativeLabels
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
       - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/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.
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
    *  - mappings
       - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - members
-      - `Variation </ga4gh/schema/vrs/2.x/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `Variation </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
    *  - type
       - string
       - 1..1
       - MUST be "CanonicalAllele"
    *  - definingContext
-      - `Allele </ga4gh/schema/vrs/2.x/json/Allele>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `Allele </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 1..1
       - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with variants on alternate reference sequences.
diff --git a/schema/cat-vrs/def/CategoricalCnv.rst b/schema/cat-vrs/def/CategoricalCnv.rst
@@ -19,39 +19,39 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
    *  - id
       - string
       - 0..1
-      - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+      - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
    *  - label
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
       - string
       - 0..1
-      - A free-text description of the Entity.
+      - A free-text description of the entity.
    *  - alternativeLabels
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
       - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/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.
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
    *  - mappings
       - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - members
-      - `Variation </ga4gh/schema/vrs/2.x/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `Variation </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
    *  - type
       - string
       - 1..1
       - MUST be "CategoricalCnv"
    *  - location
-      - `SequenceLocation </ga4gh/schema/vrs/2.x/json/SequenceLocation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `SequenceLocation </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/SequenceLocation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 1..1
-      - A `VRS Location <https://vrs.ga4gh.org/en/2.x/concepts/location/SequenceLocation.html>`_ object that represents a sequence derived from that location, and is congruent with locations  on alternate reference sequences.
+      - A `VRS Location <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08.1/concepts/location/SequenceLocation.html>`_ object that represents a sequence derived from that location, and is congruent with locations  on alternate reference sequences.
    *  - locationMatchCharacteristic
       - string
       - 0..1
@@ -61,6 +61,6 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
       - 0..1
       - A representation of the change in copies of a sequence in a system. MUST be one of "EFO:0030069" (complete  genomic loss), "EFO:0020073" (high-level loss), "EFO:0030068" (low-level loss), "EFO:0030067" (loss),  "EFO:0030064" (regional base ploidy), "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072"  (high-level gain).
    *  - copies
-      - integer | `Range </ga4gh/schema/vrs/2.x/json/Range>`_
+      - integer | `Range </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range>`_
       - 0..1
       - The integral number of copies of the subject in a system.
diff --git a/schema/cat-vrs/def/CategoricalVariation.rst b/schema/cat-vrs/def/CategoricalVariation.rst
@@ -19,32 +19,32 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core-im:Domain
    *  - id
       - string
       - 0..1
-      - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+      - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
    *  - type
       - string
       - 1..1
-      - The name of the class that is instantiated by a data object representing the Entity.
+      - 
    *  - label
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
       - string
       - 0..1
-      - A free-text description of the Entity.
+      - A free-text description of the entity.
    *  - alternativeLabels
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
       - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/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.
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
    *  - mappings
       - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - members
-      - `Variation </ga4gh/schema/vrs/2.x/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `Variation </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
diff --git a/schema/cat-vrs/def/DescribedVariation.rst b/schema/cat-vrs/def/DescribedVariation.rst
@@ -19,21 +19,21 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation
    *  - id
       - string
       - 0..1
-      - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+      - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
    *  - alternativeLabels
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
       - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/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.
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
    *  - mappings
       - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - members
-      - `Variation </ga4gh/schema/vrs/2.x/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `Variation </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
    *  - type

diff --git a/schema/cat-vrs/def/NumberChange.rst b/schema/cat-vrs/def/NumberChange.rst
@@ -20,6 +20,6 @@ A quantitative assessment of a unit within a system (e.g. genome, cell, etc.) re
       - 0..1
       - MUST be "NumberChange"
    *  - change
-      - integer | `Range </ga4gh/schema/vrs/2.x/json/Range>`_ | string
+      - integer | `Range </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range>`_ | string
       - 0..1
       - a quantitative or qualitative value of the measurement with respect to a baseline (0).  If qualitative, must be one of "EFO:0030069" (complete genomic loss), "EFO:0020073" (high-level loss), "EFO:0030068" (low-level loss), "EFO:0030067" (loss), "EFO:0030064" (regional base ploidy), "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072" (high-level gain).
diff --git a/schema/cat-vrs/def/NumberCount.rst b/schema/cat-vrs/def/NumberCount.rst
@@ -20,6 +20,6 @@ The absolute count of a discrete assayable unit (e.g. chromosome, gene, or seque
       - 0..1
       - MUST be "NumberCount"
    *  - count
-      - integer | `Range </ga4gh/schema/vrs/2.x/json/Range>`_
+      - integer | `Range </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range>`_
       - 1..1
       - The integral quantity or quantity range of the subject in a system
diff --git a/schema/cat-vrs/def/ProteinSequenceConsequence.rst b/schema/cat-vrs/def/ProteinSequenceConsequence.rst
@@ -19,36 +19,36 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV
    *  - id
       - string
       - 0..1
-      - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+      - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
    *  - label
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
       - string
       - 0..1
-      - A free-text description of the Entity.
+      - A free-text description of the entity.
    *  - alternativeLabels
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
       - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/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.
+      - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.
    *  - mappings
       - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - members
-      - `Variation </ga4gh/schema/vrs/2.x/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `Variation </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
    *  - type
       - string
       - 1..1
       - MUST be "ProteinSequenceConsequence"
    *  - definingContext
-      - `Allele </ga4gh/schema/vrs/2.x/json/Allele>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - `Allele </ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
       - 1..1
       - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with (projects to the same codons) as alleles on other protein reference  sequences.