From e8a75438ded5fc19d7435ae546537fad3501a304 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Sun, 8 Sep 2024 20:32:19 -0400 Subject: [PATCH] update submodule to vrs/common ballot. --- schema/cat-vrs/cat-vrs-source.yaml | 72 +++++++++---------- schema/cat-vrs/def/CanonicalAllele.rst | 4 +- schema/cat-vrs/def/CategoricalCnv.rst | 8 +-- schema/cat-vrs/def/CategoricalVariation.rst | 2 +- schema/cat-vrs/def/DescribedVariation.rst | 4 +- .../def/ProteinSequenceConsequence.rst | 4 +- schema/cat-vrs/json/CanonicalAllele | 16 ++--- schema/cat-vrs/json/CategoricalCnv | 22 +++--- schema/cat-vrs/json/CategoricalVariation | 2 +- schema/cat-vrs/json/DescribedVariation | 12 ++-- schema/cat-vrs/json/NumberChange | 2 +- schema/cat-vrs/json/NumberCount | 2 +- .../cat-vrs/json/ProteinSequenceConsequence | 16 ++--- submodules/vrs | 2 +- 14 files changed, 84 insertions(+), 84 deletions(-) diff --git a/schema/cat-vrs/cat-vrs-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml index bc03b31..c7597ec 100644 --- a/schema/cat-vrs/cat-vrs-source.yaml +++ b/schema/cat-vrs/cat-vrs-source.yaml @@ -22,7 +22,7 @@ $defs: inherits: gks.core-im:DomainEntity maturity: draft description: >- - A representation of a categorically-defined domain for variation, in which individual + A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain. oneOf: - $ref: "#/$defs/CanonicalAllele" @@ -38,8 +38,8 @@ $defs: this categorical variant. items: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Variation" - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" + - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI" ProteinSequenceConsequence: type: object @@ -49,8 +49,8 @@ $defs: 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. The protein sequence consequence, like a :ref:`CanonicalAllele`, is defined by an - `Allele ` that is representative of a collection - of congruent Protein Alleles that share the same altered codon(s). + `Allele ` + that is representative of a collection of congruent Protein Alleles that share the same altered codon(s). properties: type: extends: type @@ -59,11 +59,11 @@ $defs: description: 'MUST be "ProteinSequenceConsequence"' definingContext: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Allele" - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" + - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI" description: >- - The `VRS Allele `_ - object that is congruent with (projects to the same codons) as alleles on other protein reference + The `Allele `_ + object that is congruent with (projects to the same codons) as alleles on other protein reference sequences. required: - definingContext @@ -72,8 +72,8 @@ $defs: inherits: CategoricalVariation maturity: draft description: >- - A canonical allele is defined by an `Allele ` - that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid + A canonical allele is defined by an `Allele `_ + that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations. type: object @@ -85,10 +85,10 @@ $defs: description: 'MUST be "CanonicalAllele"' definingContext: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/Allele" - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" + - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI" description: >- - The `VRS Allele `_ + The `Allele `_ object that is congruent with variants on alternate reference sequences. required: - definingContext @@ -98,12 +98,12 @@ $defs: inherits: CategoricalVariation maturity: draft description: >- - A categorical variation domain is defined first by a sequence derived from a canonical `Location - `_ , which is representative of - a collection of congruent Locations. The change or count of this sequence is also described, either - by a numeric value (e.g. "3 or more copies") or categorical representation (e.g. "high-level gain"). - Categorical CNVs may optionally be defined by rules specifying the location match characteristics for - member CNVs. + A categorical variation domain is defined first by a sequence derived from a canonical `SequenceLocation + `_ , + which is representative of a collection of congruent Locations. The change or count of this sequence is + also described, either by a numeric value (e.g. "3 or more copies") or categorical representation + (e.g. "high-level gain"). Categorical CNVs may optionally be defined by rules specifying the location + match characteristics for member CNVs. properties: type: extends: type @@ -112,19 +112,19 @@ $defs: description: 'MUST be "CategoricalCnv"' location: oneOf: - - $ref: "/ga4gh/schema/vrs/2.x/json/SequenceLocation" - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/SequenceLocation" + - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI" description: >- - A `VRS Location `_ - object that represents a sequence derived from that location, and is congruent with locations + A `SequenceLocation `_ + object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences. locationMatchCharacteristic: type: string enum: ['exact', 'partial', 'subinterval', 'superinterval'] description: >- - The characteristics of a valid match between a contextual CNV location (the query) and the - Categorical CNV location (the domain), when both query and domain are represented on the same - reference sequence. An `exact` match requires the location of the query and domain to be identical. + The characteristics of a valid match between a contextual CNV location (the query) and the + Categorical CNV location (the domain), when both query and domain are represented on the same + reference sequence. An `exact` match requires the location of the query and domain to be identical. A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue of overlap between the query and domain. @@ -132,14 +132,14 @@ $defs: type: string enum: [ "EFO:0030069", "EFO:0020073", "EFO:0030068", "EFO:0030067", "EFO:0030064", "EFO:0030070", "EFO:0030071", "EFO:0030072" ] description: >- - 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" + 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: 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: @@ -163,12 +163,12 @@ $defs: label: extends: label description: >- - A primary label for the categorical variation. This required property should provide a + A primary label for the categorical variation. This required property should provide a short and descriptive textual representation of the concept. description: extends: description description: >- - A textual description of the domain of variation that should match the categorical + A textual description of the domain of variation that should match the categorical variation entity. required: - label @@ -240,7 +240,7 @@ $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" ] @@ -266,7 +266,7 @@ $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", @@ -323,7 +323,7 @@ $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 index 46c3737..69e7cea 100644 --- a/schema/cat-vrs/def/CanonicalAllele.rst +++ b/schema/cat-vrs/def/CanonicalAllele.rst @@ -1,6 +1,6 @@ **Computational Definition** -A canonical allele is defined by an `Allele ` that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations. +A canonical allele is defined by an `Allele `_ that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations. **Information Model** @@ -51,4 +51,4 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`. * - definingContext - :ref:`Allele` | :ref:`IRI` - 1..1 - - The `VRS Allele `_ object that is congruent with variants on alternate reference sequences. + - The `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 index b482d85..4cb6c65 100644 --- a/schema/cat-vrs/def/CategoricalCnv.rst +++ b/schema/cat-vrs/def/CategoricalCnv.rst @@ -1,6 +1,6 @@ **Computational Definition** -A categorical variation domain is defined first by a sequence derived from a canonical `Location `_ , which is representative of a collection of congruent Locations. The change or count of this sequence is also described, either by a numeric value (e.g. "3 or more copies") or categorical representation (e.g. "high-level gain"). Categorical CNVs may optionally be defined by rules specifying the location match characteristics for member CNVs. +A categorical variation domain is defined first by a sequence derived from a canonical `SequenceLocation `_ , which is representative of a collection of congruent Locations. The change or count of this sequence is also described, either by a numeric value (e.g. "3 or more copies") or categorical representation (e.g. "high-level gain"). Categorical CNVs may optionally be defined by rules specifying the location match characteristics for member CNVs. **Information Model** @@ -51,15 +51,15 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`. * - location - :ref:`SequenceLocation` | :ref:`IRI` - 1..1 - - A `VRS Location `_ object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences. + - A `SequenceLocation `_ object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences. * - locationMatchCharacteristic - string - 0..1 - - The characteristics of a valid match between a contextual CNV location (the query) and the Categorical CNV location (the domain), when both query and domain are represented on the same reference sequence. An `exact` match requires the location of the query and domain to be identical. A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue of overlap between the query and domain. + - The characteristics of a valid match between a contextual CNV location (the query) and the Categorical CNV location (the domain), when both query and domain are represented on the same reference sequence. An `exact` match requires the location of the query and domain to be identical. A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue of overlap between the query and domain. * - copyChange - string - 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). + - 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 | :ref:`Range` - 0..1 diff --git a/schema/cat-vrs/def/CategoricalVariation.rst b/schema/cat-vrs/def/CategoricalVariation.rst index 00dafbc..522fa8a 100644 --- a/schema/cat-vrs/def/CategoricalVariation.rst +++ b/schema/cat-vrs/def/CategoricalVariation.rst @@ -1,6 +1,6 @@ **Computational Definition** -A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain. +A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain. **Information Model** diff --git a/schema/cat-vrs/def/DescribedVariation.rst b/schema/cat-vrs/def/DescribedVariation.rst index cd728c4..79f57c1 100644 --- a/schema/cat-vrs/def/DescribedVariation.rst +++ b/schema/cat-vrs/def/DescribedVariation.rst @@ -43,8 +43,8 @@ Some DescribedVariation attributes are inherited from :ref:`CategoricalVariation * - label - string - 1..1 - - A primary label for the categorical variation. This required property should provide a short and descriptive textual representation of the concept. + - A primary label for the categorical variation. This required property should provide a short and descriptive textual representation of the concept. * - description - string - 0..1 - - A textual description of the domain of variation that should match the categorical variation entity. + - A textual description of the domain of variation that should match the categorical variation entity. diff --git a/schema/cat-vrs/def/ProteinSequenceConsequence.rst b/schema/cat-vrs/def/ProteinSequenceConsequence.rst index a2e2900..38b1e79 100644 --- a/schema/cat-vrs/def/ProteinSequenceConsequence.rst +++ b/schema/cat-vrs/def/ProteinSequenceConsequence.rst @@ -1,6 +1,6 @@ **Computational Definition** -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. The protein sequence consequence, like a :ref:`CanonicalAllele`, is defined by an `Allele ` that is representative of a collection of congruent Protein Alleles that share the same altered codon(s). +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. The protein sequence consequence, like a :ref:`CanonicalAllele`, is defined by an `Allele ` that is representative of a collection of congruent Protein Alleles that share the same altered codon(s). **Information Model** @@ -51,4 +51,4 @@ Some ProteinSequenceConsequence attributes are inherited from :ref:`CategoricalV * - definingContext - :ref:`Allele` | :ref:`IRI` - 1..1 - - The `VRS Allele `_ object that is congruent with (projects to the same codons) as alleles on other protein reference sequences. + - The `Allele `_ object that is congruent with (projects to the same codons) as alleles on other protein reference sequences. diff --git a/schema/cat-vrs/json/CanonicalAllele b/schema/cat-vrs/json/CanonicalAllele index 5601d33..1f16c92 100644 --- a/schema/cat-vrs/json/CanonicalAllele +++ b/schema/cat-vrs/json/CanonicalAllele @@ -4,7 +4,7 @@ "title": "CanonicalAllele", "type": "object", "maturity": "draft", - "description": "A canonical allele is defined by an `Allele ` that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.", + "description": "A canonical allele is defined by an [Allele](https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#) that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.", "properties": { "id": { "type": "string", @@ -31,7 +31,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." @@ -40,7 +40,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -51,10 +51,10 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } @@ -69,13 +69,13 @@ "definingContext": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" } ], - "description": "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." + "description": "The [Allele](https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#) object that is congruent with variants on alternate reference sequences." } }, "required": [ diff --git a/schema/cat-vrs/json/CategoricalCnv b/schema/cat-vrs/json/CategoricalCnv index 052f1f8..39d9cf8 100644 --- a/schema/cat-vrs/json/CategoricalCnv +++ b/schema/cat-vrs/json/CategoricalCnv @@ -4,7 +4,7 @@ "title": "CategoricalCnv", "type": "object", "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 a collection of congruent Locations. The change or count of this sequence is also described, either by a numeric value (e.g. \"3 or more copies\") or categorical representation (e.g. \"high-level gain\"). Categorical CNVs may optionally be defined by rules specifying the location match characteristics for member CNVs.", + "description": "A categorical variation domain is defined first by a sequence derived from a canonical [SequenceLocation](https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/LocationAndReference/SequenceLocation.html) , which is representative of a collection of congruent Locations. The change or count of this sequence is also described, either by a numeric value (e.g. \"3 or more copies\") or categorical representation (e.g. \"high-level gain\"). Categorical CNVs may optionally be defined by rules specifying the location match characteristics for member CNVs.", "properties": { "id": { "type": "string", @@ -31,7 +31,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -40,7 +40,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -51,10 +51,10 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } @@ -69,13 +69,13 @@ "location": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/SequenceLocation" } ], - "description": "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." + "description": "A [SequenceLocation](https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/LocationAndReference/SequenceLocation.html) object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences." }, "locationMatchCharacteristic": { "type": "string", @@ -85,7 +85,7 @@ "subinterval", "superinterval" ], - "description": "The characteristics of a valid match between a contextual CNV location (the query) and the Categorical CNV location (the domain), when both query and domain are represented on the same reference sequence. An `exact` match requires the location of the query and domain to be identical. A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue of overlap between the query and domain." + "description": "The characteristics of a valid match between a contextual CNV location (the query) and the Categorical CNV location (the domain), when both query and domain are represented on the same reference sequence. An `exact` match requires the location of the query and domain to be identical. A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue of overlap between the query and domain." }, "copyChange": { "type": "string", @@ -99,12 +99,12 @@ "EFO:0030071", "EFO:0030072" ], - "description": "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)." + "description": "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": { "oneOf": [ { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" }, { "type": "integer" diff --git a/schema/cat-vrs/json/CategoricalVariation b/schema/cat-vrs/json/CategoricalVariation index f33b25a..3070cae 100644 --- a/schema/cat-vrs/json/CategoricalVariation +++ b/schema/cat-vrs/json/CategoricalVariation @@ -4,7 +4,7 @@ "title": "CategoricalVariation", "type": "object", "maturity": "draft", - "description": "A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain.", + "description": "A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain.", "oneOf": [ { "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CanonicalAllele" diff --git a/schema/cat-vrs/json/DescribedVariation b/schema/cat-vrs/json/DescribedVariation index dfacdba..255b4aa 100644 --- a/schema/cat-vrs/json/DescribedVariation +++ b/schema/cat-vrs/json/DescribedVariation @@ -23,7 +23,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -32,7 +32,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -43,10 +43,10 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } @@ -60,11 +60,11 @@ }, "label": { "type": "string", - "description": "A primary label for the categorical variation. This required property should provide a short and descriptive textual representation of the concept." + "description": "A primary label for the categorical variation. This required property should provide a short and descriptive textual representation of the concept." }, "description": { "type": "string", - "description": "A textual description of the domain of variation that should match the categorical variation entity." + "description": "A textual description of the domain of variation that should match the categorical variation entity." } }, "required": [ diff --git a/schema/cat-vrs/json/NumberChange b/schema/cat-vrs/json/NumberChange index 6cd1885..589e273 100644 --- a/schema/cat-vrs/json/NumberChange +++ b/schema/cat-vrs/json/NumberChange @@ -15,7 +15,7 @@ "change": { "oneOf": [ { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" }, { "type": "integer" diff --git a/schema/cat-vrs/json/NumberCount b/schema/cat-vrs/json/NumberCount index 7f402bd..299678d 100644 --- a/schema/cat-vrs/json/NumberCount +++ b/schema/cat-vrs/json/NumberCount @@ -15,7 +15,7 @@ "count": { "oneOf": [ { - "$ref": "/ga4gh/schema/vrs/2.x/json/Range" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range" }, { "type": "integer" diff --git a/schema/cat-vrs/json/ProteinSequenceConsequence b/schema/cat-vrs/json/ProteinSequenceConsequence index 9f599a2..8955787 100644 --- a/schema/cat-vrs/json/ProteinSequenceConsequence +++ b/schema/cat-vrs/json/ProteinSequenceConsequence @@ -4,7 +4,7 @@ "title": "ProteinSequenceConsequence", "type": "object", "maturity": "draft", - "description": "A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a CanonicalAllele, is defined by an `Allele ` that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).", + "description": "A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a CanonicalAllele, is defined by an `Allele ` that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).", "properties": { "id": { "type": "string", @@ -31,7 +31,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/Extension" }, "description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.", "$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." @@ -40,7 +40,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -51,10 +51,10 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Variation" } ] } @@ -69,13 +69,13 @@ "definingContext": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.0.0-ballot.2024.08.1/data-types/json/IRI" }, { - "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" + "$ref": "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele" } ], - "description": "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." + "description": "The [Allele](https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#) object that is congruent with (projects to the same codons) as alleles on other protein reference sequences." } }, "required": [ diff --git a/submodules/vrs b/submodules/vrs index 1a28939..5411cac 160000 --- a/submodules/vrs +++ b/submodules/vrs @@ -1 +1 @@ -Subproject commit 1a289392665a562983ff44ea512c371491338b3d +Subproject commit 5411cac823b7d2cde7183852b439697f019f62a5