diff --git a/schema/catvrs/catvrs-source.yaml b/schema/catvrs/catvrs-source.yaml index 536445a..736b53a 100644 --- a/schema/catvrs/catvrs-source.yaml +++ b/schema/catvrs/catvrs-source.yaml @@ -5,12 +5,12 @@ type: object strict: true imports: - gks.core: ../gks-core-im/core-im-source.yaml + gks.common: ../gks-common/common-source.yaml vrs: ../vrs/vrs-source.yaml namespaces: vrs: ../vrs/vrs.yaml#/$defs/ - gks.core: ../gks-core-im/core-im.yaml#/$defs/ + gks.common: ../gks-common/common.yaml#/$defs/ $defs: # Categorical Variation are presented top-down. Everything rolls up to @@ -22,7 +22,7 @@ $defs: # ============================================================================= CategoricalVariation: - inherits: gks.core:DomainEntity + inherits: gks.common:DomainEntity description: >- A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain. @@ -41,7 +41,7 @@ $defs: items: oneOf: - $refCurie: vrs:Variation - - $refCurie: gks.core:IRI + - $refCurie: gks.common:IRI ProteinSequenceConsequence: maturity: draft @@ -55,14 +55,14 @@ $defs: of congruent Protein Alleles that share the same altered codon(s). properties: type: - type: string + extends: type const: ProteinSequenceConsequence default: ProteinSequenceConsequence description: 'MUST be "ProteinSequenceConsequence"' definingContext: oneOf: - $refCurie: vrs:Allele - - $refCurie: gks.core:IRI + - $refCurie: gks.common:IRI description: >- The `VRS Allele `_ object that is congruent with (projects to the same codons) as alleles on other protein reference @@ -81,14 +81,14 @@ $defs: type: object properties: type: - type: string + extends: type const: CanonicalAllele default: CanonicalAllele description: 'MUST be "CanonicalAllele"' definingContext: oneOf: - $refCurie: vrs:Allele - - $refCurie: gks.core:IRI + - $refCurie: gks.common:IRI description: >- The `VRS Allele `_ object that is congruent with variants on alternate reference sequences. @@ -108,7 +108,7 @@ $defs: member CNVs. properties: type: - type: string + extends: type const: CategoricalCnv default: CategoricalCnv description: 'MUST be "CategoricalCnv"' @@ -157,7 +157,7 @@ $defs: to indicate how a categorical variation concept should be evaluated for matching variants. properties: type: - type: string + extends: type const: DescribedVariation default: DescribedVariation description: 'MUST be "DescribedVariation"' @@ -342,7 +342,7 @@ $defs: # ============================================================================= CategoricalVariant: - inherits: gks.core:DomainEntity + inherits: gks.common:DomainEntity 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 @@ -363,7 +363,7 @@ $defs: # type: array # ordered: true # items: - # - $refExtension: gks.core:Extension + # - $refExtension: gks.common:Extension diff --git a/schema/catvrs/def/CanonicalAllele.rst b/schema/catvrs/def/CanonicalAllele.rst index 10ca105..af2cdad 100644 --- a/schema/catvrs/def/CanonicalAllele.rst +++ b/schema/catvrs/def/CanonicalAllele.rst @@ -33,22 +33,22 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - `Extension <../gks-core-im/core.json#/$defs/Extension>`_ + - `Extension <../gks-common/common.json#/$defs/Extension>`_ - 0..m - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. - * - type - - string - - 1..1 - - MUST be "CanonicalAllele" * - mappings - - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_ + - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_ + - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. + * - type + - string + - 1..1 + - MUST be "CanonicalAllele" * - definingContext - - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_ + - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_ - 1..1 - The `VRS Allele `_ object that is congruent with variants on alternate reference sequences. diff --git a/schema/catvrs/def/CategoricalCnv.rst b/schema/catvrs/def/CategoricalCnv.rst index 57916fa..516a918 100644 --- a/schema/catvrs/def/CategoricalCnv.rst +++ b/schema/catvrs/def/CategoricalCnv.rst @@ -33,21 +33,21 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`. - 0..m - Alternative name(s) for the Entity. * - extensions - - `Extension <../gks-core-im/core.json#/$defs/Extension>`_ + - `Extension <../gks-common/common.json#/$defs/Extension>`_ - 0..m - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. - * - type - - string - - 1..1 - - MUST be "CategoricalCnv" * - mappings - - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_ + - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_ + - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. + * - type + - string + - 1..1 + - MUST be "CategoricalCnv" * - location - {'$ref': '../vrs/vrs.yaml#/$defs/Location'} - 1..1 diff --git a/schema/catvrs/def/CategoricalVariation.rst b/schema/catvrs/def/CategoricalVariation.rst index 85e0e01..89eef7a 100644 --- a/schema/catvrs/def/CategoricalVariation.rst +++ b/schema/catvrs/def/CategoricalVariation.rst @@ -4,7 +4,7 @@ A representation of a categorically-defined domain for variation, in which indiv **Information Model** -Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEntity`. +Some CategoricalVariation attributes are inherited from :ref:`gks.common:DomainEntity`. .. list-table:: :class: clean-wrap @@ -20,6 +20,10 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEnt - string - 0..1 - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE). + * - type + - string + - 1..1 + - * - label - string - 0..1 @@ -33,18 +37,14 @@ Some CategoricalVariation attributes are inherited from :ref:`gks.core:DomainEnt - 0..m - Alternative name(s) for the Entity. * - extensions - - `Extension <../gks-core-im/core.json#/$defs/Extension>`_ + - `Extension <../gks-common/common.json#/$defs/Extension>`_ - 0..m - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. - * - type - - string - - 1..1 - - * - mappings - - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_ + - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_ + - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. diff --git a/schema/catvrs/def/DescribedVariation.rst b/schema/catvrs/def/DescribedVariation.rst index f7f05ab..398092b 100644 --- a/schema/catvrs/def/DescribedVariation.rst +++ b/schema/catvrs/def/DescribedVariation.rst @@ -25,21 +25,21 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation - 0..m - Alternative name(s) for the Entity. * - extensions - - `Extension <../gks-core-im/core.json#/$defs/Extension>`_ + - `Extension <../gks-common/common.json#/$defs/Extension>`_ - 0..m - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. - * - type - - string - - 1..1 - - MUST be "DescribedVariation" * - mappings - - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_ + - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_ + - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. + * - type + - string + - 1..1 + - MUST be "DescribedVariation" * - label - string - 1..1 diff --git a/schema/catvrs/def/ProteinSequenceConsequence.rst b/schema/catvrs/def/ProteinSequenceConsequence.rst index 5897ad3..0df07b2 100644 --- a/schema/catvrs/def/ProteinSequenceConsequence.rst +++ b/schema/catvrs/def/ProteinSequenceConsequence.rst @@ -33,22 +33,22 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV - 0..m - Alternative name(s) for the Entity. * - extensions - - `Extension <../gks-core-im/core.json#/$defs/Extension>`_ + - `Extension <../gks-common/common.json#/$defs/Extension>`_ - 0..m - A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems. - * - type - - string - - 1..1 - - MUST be "ProteinSequenceConsequence" * - mappings - - `ConceptMapping <../gks-core-im/core.json#/$defs/ConceptMapping>`_ + - `ConceptMapping <../gks-common/common.json#/$defs/ConceptMapping>`_ - 0..m - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation. * - members - - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_ + - `Variation <../vrs/vrs.yaml#/$defs/Variation>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_ - 0..m - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant. + * - type + - string + - 1..1 + - MUST be "ProteinSequenceConsequence" * - definingContext - - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-core-im/core-im.yaml#/$defs/IRI>`_ + - `Allele <../vrs/vrs.yaml#/$defs/Allele>`_ | `IRI <../gks-common/common.yaml#/$defs/IRI>`_ - 1..1 - The `VRS Allele `_ object that is congruent with (projects to the same codons) as alleles on other protein reference sequences. diff --git a/schema/catvrs/json/CanonicalAllele b/schema/catvrs/json/CanonicalAllele index f90cb26..b385e9c 100644 --- a/schema/catvrs/json/CanonicalAllele +++ b/schema/catvrs/json/CanonicalAllele @@ -30,21 +30,15 @@ "type": "array", "ordered": true, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" }, "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "type": { - "type": "string", - "const": "CanonicalAllele", - "default": "CanonicalAllele", - "description": "MUST be \"CanonicalAllele\"" - }, "mappings": { "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.x/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -55,7 +49,7 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" @@ -63,10 +57,16 @@ ] } }, + "type": { + "type": "string", + "const": "CanonicalAllele", + "default": "CanonicalAllele", + "description": "MUST be \"CanonicalAllele\"" + }, "definingContext": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" diff --git a/schema/catvrs/json/CategoricalCnv b/schema/catvrs/json/CategoricalCnv index c465db5..141e6f6 100644 --- a/schema/catvrs/json/CategoricalCnv +++ b/schema/catvrs/json/CategoricalCnv @@ -30,21 +30,15 @@ "type": "array", "ordered": true, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" }, "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "type": { - "type": "string", - "const": "CategoricalCnv", - "default": "CategoricalCnv", - "description": "MUST be \"CategoricalCnv\"" - }, "mappings": { "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.x/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -55,7 +49,7 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" @@ -63,6 +57,12 @@ ] } }, + "type": { + "type": "string", + "const": "CategoricalCnv", + "default": "CategoricalCnv", + "description": "MUST be \"CategoricalCnv\"" + }, "location": { "type": { "$ref": "/ga4gh/schema/vrs/2.x/json/Location" diff --git a/schema/catvrs/json/DescribedVariation b/schema/catvrs/json/DescribedVariation index b0aeee2..7a4382e 100644 --- a/schema/catvrs/json/DescribedVariation +++ b/schema/catvrs/json/DescribedVariation @@ -22,21 +22,15 @@ "type": "array", "ordered": true, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" }, "description": "A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." }, - "type": { - "type": "string", - "const": "DescribedVariation", - "default": "DescribedVariation", - "description": "MUST be \"DescribedVariation\"" - }, "mappings": { "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.x/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -47,7 +41,7 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" @@ -55,6 +49,12 @@ ] } }, + "type": { + "type": "string", + "const": "DescribedVariation", + "default": "DescribedVariation", + "description": "MUST be \"DescribedVariation\"" + }, "label": { "type": "string", "description": "A primary label for the categorical variation. This required property should provide a short and descriptive textual representation of the concept." diff --git a/schema/catvrs/json/ProteinSequenceConsequence b/schema/catvrs/json/ProteinSequenceConsequence index df1810e..880b8ad 100644 --- a/schema/catvrs/json/ProteinSequenceConsequence +++ b/schema/catvrs/json/ProteinSequenceConsequence @@ -30,21 +30,15 @@ "type": "array", "ordered": true, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.x/json/Extension" }, "description": "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." }, - "type": { - "type": "string", - "const": "ProteinSequenceConsequence", - "default": "ProteinSequenceConsequence", - "description": "MUST be \"ProteinSequenceConsequence\"" - }, "mappings": { "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.x/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -55,7 +49,7 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" @@ -63,10 +57,16 @@ ] } }, + "type": { + "type": "string", + "const": "ProteinSequenceConsequence", + "default": "ProteinSequenceConsequence", + "description": "MUST be \"ProteinSequenceConsequence\"" + }, "definingContext": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-core-im/1.x/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" diff --git a/schema/gks-common b/schema/gks-common new file mode 120000 index 0000000..15afdee --- /dev/null +++ b/schema/gks-common @@ -0,0 +1 @@ +../submodules/vrs/schema/gks-common/ \ No newline at end of file diff --git a/schema/gks-core-im b/schema/gks-core-im deleted file mode 120000 index 0c3b84e..0000000 --- a/schema/gks-core-im +++ /dev/null @@ -1 +0,0 @@ -../submodules/vrs/schema/gks-core-im \ No newline at end of file diff --git a/schema/gks-domain-entities b/schema/gks-domain-entities deleted file mode 120000 index 940a2fa..0000000 --- a/schema/gks-domain-entities +++ /dev/null @@ -1 +0,0 @@ -../submodules/vrs/schema/gks-domain-entities \ No newline at end of file diff --git a/submodules/vrs b/submodules/vrs index 2018884..ca30180 160000 --- a/submodules/vrs +++ b/submodules/vrs @@ -1 +1 @@ -Subproject commit 2018884bb5181aed47cb2ae6ffa1aebba39619f6 +Subproject commit ca3018094397d62025a65b12c991c6189f4275af