update MSP / submodule

.requirements.txt

@@ -2,6 +2,6 @@ pytest
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2
 pyyaml
-ga4gh.gks.metaschema==0.3.0b11
+ga4gh.gks.metaschema==0.3.0b12
 jsonschema
 referencing

schema/cat-vrs/cat-vrs-source.yaml

@@ -20,6 +20,7 @@ $defs:
 
   CategoricalVariation:
     inherits: gks.core-im:DomainEntity
+    maturity: draft
     description: >-
       A representation of a categorically-defined domain for variation, in which individual 
       contextual variation instances may be members of the domain.
@@ -41,9 +42,9 @@ $defs:
             - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
 
   ProteinSequenceConsequence:
-    maturity: draft
     type: object
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
       A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature
       of the genetic code, there are often several genomic changes that can cause a protein sequence consequence.
@@ -68,8 +69,8 @@ $defs:
       - definingContext
 
   CanonicalAllele:
-    maturity: draft
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
       A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#variation>` 
       that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid 
@@ -93,9 +94,9 @@ $defs:
       - definingContext
 
   CategoricalCnv:
-    maturity: draft
     type: object
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
       A categorical variation domain is defined first by a sequence derived from a canonical `Location 
       <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#Location>`_ , which is representative of 
@@ -145,9 +146,9 @@ $defs:
       - location
 
   DescribedVariation:
-    maturity: draft
     type: object
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
       Some categorical variation concepts are supported by custom nomenclatures or text-descriptive
       representations for which a categorical variation model does not exist. DescribedVariation is
@@ -221,12 +222,12 @@ $defs:
 
 
   NumberCount:
-    maturity: draft
     # ga4ghDigest:
     #   keys:
     #     - numberCount
     type: object
     # inherits: QuantityVariance
+    maturity: draft
     description: >-
       The absolute count of a discrete assayable unit (e.g. chromosome, gene, or sequence).
     properties:
@@ -246,12 +247,12 @@ $defs:
 
 
   NumberChange:
-    maturity: draft
     # ga4ghDigest:
     #   keys:
     #     - numberChange
     #   prefix: CX
     type: object
+    maturity: draft
     description: >-
       A quantitative assessment of a unit within a system (e.g. genome, cell,
       etc.) relative to a baseline quantity.
@@ -278,9 +279,9 @@ $defs:
         required: [ "change" ]
 
   QuantityVariance:
-    maturity: draft
     type: object
     # inherits: NumberCount
+    maturity: draft
     description: >-
       The Quantity Variance class captures one axis of variation in the generalized model of categorical
       variation.  It is used to model quantitative measure changes in a given biological level of
@@ -340,6 +341,7 @@ $defs:
 
   CategoricalVariant:
     inherits: gks.core-im:DomainEntity
+    maturity: draft
     description: >-
       A top-level representation of a categorically-defined domain for variation across one or multiple biological levels in which individual contextual variants may be members of the domain.
     # type: object

schema/cat-vrs/def/CanonicalAllele.rst

@@ -33,22 +33,22 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - :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.
    *  - mappings
-      - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
+      - :ref:`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>`_
+      - :ref:`Variation` | :ref:`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>`_
+      - :ref:`Allele` | :ref:`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.

schema/cat-vrs/def/CategoricalCnv.rst

@@ -33,23 +33,23 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - :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.
    *  - mappings
-      - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
+      - :ref:`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>`_
+      - :ref:`Variation` | :ref:`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>`_
+      - :ref:`SequenceLocation` | :ref:`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.
    *  - locationMatchCharacteristic
@@ -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 | :ref:`Range`
       - 0..1
       - The integral number of copies of the subject in a system.

schema/cat-vrs/def/CategoricalVariation.rst

@@ -37,14 +37,14 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core-im:Domain
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - :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.
    *  - mappings
-      - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
+      - :ref:`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>`_
+      - :ref:`Variation` | :ref:`IRI`
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.

schema/cat-vrs/def/DescribedVariation.rst

@@ -25,15 +25,15 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - :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.
    *  - mappings
-      - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
+      - :ref:`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>`_
+      - :ref:`Variation` | :ref:`IRI`
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
    *  - type

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 | :ref:`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).

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 | :ref:`Range`
       - 1..1
       - The integral quantity or quantity range of the subject in a system

schema/cat-vrs/def/ProteinSequenceConsequence.rst

@@ -33,22 +33,22 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - :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.
    *  - mappings
-      - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
+      - :ref:`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>`_
+      - :ref:`Variation` | :ref:`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>`_
+      - :ref:`Allele` | :ref:`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.

schema/cat-vrs/json/CategoricalVariation

@@ -3,6 +3,7 @@
    "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariation",
    "title": "CategoricalVariation",
    "type": "object",
+   "maturity": "draft",
    "description": "A representation of a categorically-defined domain for variation, in which individual  contextual variation instances may be members of the domain.",
    "oneOf": [
       {