From 6b8b86f2f91a84e91ac567ff4b9ffbc67baf300b Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Fri, 1 Mar 2024 17:50:34 -0500 Subject: [PATCH 1/3] update maturity model --- schema/merged.json | 54 ++++++------- schema/merged.yaml | 54 ++++++------- schema/vrs-source.yaml | 169 ++++++++++++++++++++--------------------- schema/vrs.json | 28 +++---- schema/vrs.yaml | 28 +++---- submodules/gks-common | 2 +- 6 files changed, 166 insertions(+), 169 deletions(-) diff --git a/schema/merged.json b/schema/merged.json index 4ad333ce..e7e03a0f 100644 --- a/schema/merged.json +++ b/schema/merged.json @@ -32,7 +32,7 @@ "Expression": { "type": "object", "privateTo": "Variation", - "maturity": "Alpha", + "maturity": "draft", "description": "Representation of a variation by a specified nomenclature or syntax for a Variation object. Common examples of expressions for the description of molecular variation include the HGVS and ISCN nomenclatures.", "properties": { "syntax": { @@ -94,7 +94,7 @@ } }, "Allele": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "prefix": "VA", "keys": [ @@ -176,7 +176,7 @@ "additionalProperties": false }, "Haplotype": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "prefix": "HT", "keys": [ @@ -251,7 +251,7 @@ "additionalProperties": false }, "CopyNumberCount": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "copies", @@ -330,7 +330,7 @@ "additionalProperties": false }, "CopyNumberChange": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "copyChange", @@ -490,7 +490,7 @@ "additionalProperties": false }, "SequenceLocation": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "end", @@ -571,7 +571,7 @@ "additionalProperties": false }, "SequenceReference": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "assigned": true }, @@ -640,7 +640,7 @@ } }, "ReferenceLengthExpression": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "length", @@ -709,7 +709,7 @@ "additionalProperties": false }, "LengthExpression": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "length", @@ -766,7 +766,7 @@ "additionalProperties": false }, "LiteralSequenceExpression": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "sequence", @@ -882,7 +882,7 @@ "additionalProperties": false }, "Range": { - "maturity": "Alpha", + "maturity": "draft", "description": "An inclusive range of values bounded by one or more integers.", "type": "array", "ordered": true, @@ -900,19 +900,19 @@ "minItems": 2 }, "Residue": { - "maturity": "Alpha", + "maturity": "draft", "description": "A character representing a specific residue (i.e., molecular species) or groupings of these (\"ambiguity codes\"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids.", "type": "string", "pattern": "[A-Z*\\-]" }, "SequenceString": { - "maturity": "Alpha", + "maturity": "draft", "description": "A character string of Residues that represents a biological sequence using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.", "type": "string", "pattern": "^[A-Z*\\-]*$" }, "Adjacency": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "prefix": "AJ", "keys": [ @@ -1001,7 +1001,7 @@ }, "Coding": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "a concept codified by a terminology system.", "properties": { "label": { @@ -1029,7 +1029,7 @@ }, "Mapping": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "A mapping to a concept in a terminology system.", "properties": { "id": { @@ -1074,7 +1074,7 @@ }, "Extension": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "The Extension class provides VODs with a means to extend descriptions with other attributes unique to a content provider. These extensions are not expected to be natively understood under VRSATILE, but may be used for pre-negotiated exchange of message attributes when needed.", "properties": { "type": { @@ -1104,14 +1104,14 @@ "additionalProperties": false }, "Code": { - "maturity": "Alpha", + "maturity": "draft", "description": "Indicates that the value is taken from a set of controlled strings defined elsewhere. Technically, a code is restricted to a string which has at least one character and no leading or trailing whitespace, and where there is no whitespace other than single spaces in the contents.", "type": "string", "pattern": "\\S+( \\S+)*", "example": "ENSG00000139618" }, "IRI": { - "maturity": "Alpha", + "maturity": "draft", "description": "An IRI Reference (either an IRI or a relative-reference), according to `RFC3986 section 4.1 ` and `RFC3987 section 2.1 `. MAY be a JSON Pointer as an IRI fragment, as described by `RFC6901 section 6 `.", "type": "string", "format": "iri-reference" @@ -1132,7 +1132,7 @@ }, "TraitSet": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "A set of phenotype and/or disease concepts that together constitute a condition.", "properties": { "id": { @@ -1199,7 +1199,7 @@ }, "Disease": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "A particular abnormal condition that negatively affects the structure or function of all or part of an organism and is not immediately due to any external injury.", "properties": { "id": { @@ -1250,7 +1250,7 @@ }, "Phenotype": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "An observable characteristic or trait of an organism.", "properties": { "id": { @@ -1318,7 +1318,7 @@ }, "TherapeuticAction": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "A therapeutic action taken that is intended to alter or stop a pathologic process.", "properties": { "id": { @@ -1369,7 +1369,7 @@ }, "TherapeuticAgent": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "An administered therapeutic agent that is intended to alter or stop a pathologic process.", "properties": { "id": { @@ -1420,7 +1420,7 @@ }, "CombinationTherapy": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "A therapeutic procedure that involves multiple different therapeutic procedures performed in combination.", "properties": { "id": { @@ -1491,7 +1491,7 @@ }, "TherapeuticSubstituteGroup": { "type": "object", - "maturity": "Alpha", + "maturity": "draft", "description": "A group of therapeutic procedures that may be treated as substitutes for one another.", "properties": { "id": { @@ -1558,7 +1558,7 @@ "additionalProperties": false }, "Gene": { - "maturity": "Alpha", + "maturity": "draft", "description": "A basic physical and functional unit of heredity.", "type": "object", "properties": { diff --git a/schema/merged.yaml b/schema/merged.yaml index 4b9e64b5..7608fc1b 100644 --- a/schema/merged.yaml +++ b/schema/merged.yaml @@ -16,7 +16,7 @@ $defs: Expression: type: object privateTo: Variation - maturity: Alpha + maturity: draft description: Representation of a variation by a specified nomenclature or syntax for a Variation object. Common examples of expressions for the description of molecular variation include the HGVS and ISCN nomenclatures. @@ -58,7 +58,7 @@ $defs: discriminator: propertyName: type Allele: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: VA keys: @@ -116,7 +116,7 @@ $defs: - state additionalProperties: false Haplotype: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: HT keys: @@ -179,7 +179,7 @@ $defs: - members additionalProperties: false CopyNumberCount: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - copies @@ -237,7 +237,7 @@ $defs: - location additionalProperties: false CopyNumberChange: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - copyChange @@ -369,7 +369,7 @@ $defs: - members additionalProperties: false SequenceLocation: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - end @@ -429,7 +429,7 @@ $defs: required: [] additionalProperties: false SequenceReference: - maturity: Alpha + maturity: draft ga4ghDigest: assigned: true type: object @@ -484,7 +484,7 @@ $defs: discriminator: propertyName: type ReferenceLengthExpression: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - length @@ -537,7 +537,7 @@ $defs: - type additionalProperties: false LengthExpression: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - length @@ -580,7 +580,7 @@ $defs: - type additionalProperties: false LiteralSequenceExpression: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - sequence @@ -669,7 +669,7 @@ $defs: - variation additionalProperties: false Range: - maturity: Alpha + maturity: draft description: An inclusive range of values bounded by one or more integers. type: array ordered: true @@ -680,14 +680,14 @@ $defs: maxItems: 2 minItems: 2 Residue: - maturity: Alpha + maturity: draft description: A character representing a specific residue (i.e., molecular species) or groupings of these ("ambiguity codes"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids. type: string pattern: '[A-Z*\-]' SequenceString: - maturity: Alpha + maturity: draft description: "A character string of Residues that represents a biological sequence\ \ using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid\ \ sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity\ @@ -695,7 +695,7 @@ $defs: type: string pattern: ^[A-Z*\-]*$ Adjacency: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: AJ keys: @@ -762,7 +762,7 @@ $defs: additionalProperties: false Coding: type: object - maturity: Alpha + maturity: draft description: a concept codified by a terminology system. properties: label: @@ -783,7 +783,7 @@ $defs: additionalProperties: false Mapping: type: object - maturity: Alpha + maturity: draft description: A mapping to a concept in a terminology system. properties: id: @@ -821,7 +821,7 @@ $defs: additionalProperties: false Extension: type: object - maturity: Alpha + maturity: draft description: The Extension class provides VODs with a means to extend descriptions with other attributes unique to a content provider. These extensions are not expected to be natively understood under VRSATILE, but may be used for pre-negotiated @@ -847,7 +847,7 @@ $defs: - name additionalProperties: false Code: - maturity: Alpha + maturity: draft description: Indicates that the value is taken from a set of controlled strings defined elsewhere. Technically, a code is restricted to a string which has at least one character and no leading or trailing whitespace, and where there @@ -856,7 +856,7 @@ $defs: pattern: \S+( \S+)* example: ENSG00000139618 IRI: - maturity: Alpha + maturity: draft description: An IRI Reference (either an IRI or a relative-reference), according to `RFC3986 section 4.1 ` and `RFC3987 section 2.1 `. @@ -872,7 +872,7 @@ $defs: - $ref: '#/$defs/TraitSet' TraitSet: type: object - maturity: Alpha + maturity: draft description: A set of phenotype and/or disease concepts that together constitute a condition. properties: @@ -923,7 +923,7 @@ $defs: additionalProperties: false Disease: type: object - maturity: Alpha + maturity: draft description: A particular abnormal condition that negatively affects the structure or function of all or part of an organism and is not immediately due to any external injury. @@ -966,7 +966,7 @@ $defs: additionalProperties: false Phenotype: type: object - maturity: Alpha + maturity: draft description: An observable characteristic or trait of an organism. properties: id: @@ -1015,7 +1015,7 @@ $defs: - $ref: '#/$defs/TherapeuticSubstituteGroup' TherapeuticAction: type: object - maturity: Alpha + maturity: draft description: A therapeutic action taken that is intended to alter or stop a pathologic process. properties: @@ -1057,7 +1057,7 @@ $defs: additionalProperties: false TherapeuticAgent: type: object - maturity: Alpha + maturity: draft description: An administered therapeutic agent that is intended to alter or stop a pathologic process. properties: @@ -1099,7 +1099,7 @@ $defs: additionalProperties: false CombinationTherapy: type: object - maturity: Alpha + maturity: draft description: A therapeutic procedure that involves multiple different therapeutic procedures performed in combination. properties: @@ -1153,7 +1153,7 @@ $defs: additionalProperties: false TherapeuticSubstituteGroup: type: object - maturity: Alpha + maturity: draft description: A group of therapeutic procedures that may be treated as substitutes for one another. properties: @@ -1205,7 +1205,7 @@ $defs: - type additionalProperties: false Gene: - maturity: Alpha + maturity: draft description: A basic physical and functional unit of heredity. type: object properties: diff --git a/schema/vrs-source.yaml b/schema/vrs-source.yaml index c5a80642..ce71b4d6 100644 --- a/schema/vrs-source.yaml +++ b/schema/vrs-source.yaml @@ -31,14 +31,8 @@ $defs: ValueObject: inherits: gks.core:Entity description: >- - A contextual value whose equality is based on value, not identity. All VRS Value Objects - may have computed digests from the VRS Computed Identifier algorithm. + A contextual value whose equality is based on value, not identity. See https://en.wikipedia.org/wiki/Value_object for more on Value Objects. - heritableProperties: - digest: - description: A sha512t24u digest created using the VRS Computed Identifier algorithm. - type: string - pattern: '^[0-9A-Za-z_\-]{32}$' Ga4ghIdentifiableObject: inherits: ValueObject @@ -50,6 +44,10 @@ $defs: heritableProperties: type: type: string + digest: + description: A sha512t24u digest created using the VRS Computed Identifier algorithm. + type: string + pattern: '^[0-9A-Za-z_\-]{32}$' Variation: inherits: Ga4ghIdentifiableObject @@ -70,7 +68,7 @@ $defs: Expression: type: object privateTo: Variation - maturity: Alpha + maturity: draft description: >- Representation of a variation by a specified nomenclature or syntax for a Variation object. Common examples of expressions for the description of molecular variation include the HGVS @@ -103,7 +101,6 @@ $defs: A Variation of multiple molecules in the context of a system, e.g. a genome, sample, or homologous chromosomes. oneOf: - - $ref: "#/$defs/Genotype" - $ref: "#/$defs/CopyNumberCount" - $ref: "#/$defs/CopyNumberChange" discriminator: @@ -118,7 +115,7 @@ $defs: # Molecular Variation Allele: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: VA keys: @@ -148,7 +145,7 @@ $defs: required: [ "location", "state" ] Haplotype: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: HT keys: @@ -204,7 +201,7 @@ $defs: heritableRequired: [ "location" ] CopyNumberCount: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - copies @@ -230,7 +227,7 @@ $defs: required: [ "copies" ] CopyNumberChange: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - copyChange @@ -257,45 +254,45 @@ $defs: "efo:0030070" (gain), "efo:0030071" (low-level gain), "efo:0030072" (high-level gain). required: [ "copyChange" ] - Genotype: - maturity: Alpha - ga4ghDigest: - keys: - - members - - count - prefix: GT - inherits: SystemicVariation - description: >- - A quantified set of _in-trans_ :ref:`MolecularVariation` at a genomic locus. - type: object - properties: - type: - type: string - const: "Genotype" - default: "Genotype" - description: >- - MUST be "Genotype" - members: - type: array - ordered: false - uniqueItems: true - minItems: 1 - items: - $ref: "#/$defs/GenotypeMember" - description: >- - Each GenotypeMember in `members` describes a :ref:`MolecularVariation` - and the count of that variation at the locus. - count: - oneOf: - - type: integer - - $ref: "#/$defs/Range" - description: >- - The total number of copies of all :ref:`MolecularVariation` at this locus, - MUST be greater than or equal to the sum of :ref:`GenotypeMember` copy counts. - If greater than the total counts, this implies additional - :ref:`MolecularVariation` that are expected to exist but are not explicitly - indicated. - required: [ "members", "count" ] +# Genotype: +# maturity: draft +# ga4ghDigest: +# keys: +# - members +# - count +# prefix: GT +# inherits: SystemicVariation +# description: >- +# A quantified set of _in-trans_ :ref:`MolecularVariation` at a genomic locus. +# type: object +# properties: +# type: +# type: string +# const: "Genotype" +# default: "Genotype" +# description: >- +# MUST be "Genotype" +# members: +# type: array +# ordered: false +# uniqueItems: true +# minItems: 1 +# items: +# $ref: "#/$defs/GenotypeMember" +# description: >- +# Each GenotypeMember in `members` describes a :ref:`MolecularVariation` +# and the count of that variation at the locus. +# count: +# oneOf: +# - type: integer +# - $ref: "#/$defs/Range" +# description: >- +# The total number of copies of all :ref:`MolecularVariation` at this locus, +# MUST be greater than or equal to the sum of :ref:`GenotypeMember` copy counts. +# If greater than the total counts, this implies additional +# :ref:`MolecularVariation` that are expected to exist but are not explicitly +# indicated. +# required: [ "members", "count" ] # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Locations @@ -309,7 +306,7 @@ $defs: propertyName: type SequenceLocation: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - start @@ -349,7 +346,7 @@ $defs: MUST represent a coordinate or range greater than or equal to the value of `start`. SequenceReference: - maturity: Alpha + maturity: draft inherits: ValueObject ga4ghDigest: assigned: true # This special property indicates that the `digest` field follows an alternate convention @@ -412,7 +409,7 @@ $defs: - type ReferenceLengthExpression: - maturity: Alpha + maturity: draft inherits: SequenceExpression ga4ghDigest: keys: @@ -443,7 +440,7 @@ $defs: - repeatSubunitLength LengthExpression: - maturity: Alpha + maturity: draft inherits: SequenceExpression ga4ghDigest: keys: @@ -462,7 +459,7 @@ $defs: - type: integer LiteralSequenceExpression: - maturity: Alpha + maturity: draft inherits: SequenceExpression ga4ghDigest: keys: @@ -484,37 +481,37 @@ $defs: # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Nested Classes - GenotypeMember: - privateTo: Genotype - inherits: ValueObject - ga4ghDigest: - keys: - - count - - variation - description: >- - A class for expressing the count of a specific :ref:`MolecularVariation` present - _in-trans_ at a genomic locus represented by a :ref:`Genotype`. - type: object - properties: - count: - oneOf: - - $ref: '#/$defs/Range' - - type: integer - description: >- - The number of copies of the `variation` at a :ref:`Genotype` locus. - variation: - oneOf: - - $ref: "#/$defs/Allele" - - $ref: "#/$defs/Haplotype" - description: >- - A :ref:`MolecularVariation` at a :ref:`Genotype` locus. - required: [ "count", "variation" ] +# GenotypeMember: +# privateTo: Genotype +# inherits: ValueObject +# ga4ghDigest: +# keys: +# - count +# - variation +# description: >- +# A class for expressing the count of a specific :ref:`MolecularVariation` present +# _in-trans_ at a genomic locus represented by a :ref:`Genotype`. +# type: object +# properties: +# count: +# oneOf: +# - $ref: '#/$defs/Range' +# - type: integer +# description: >- +# The number of copies of the `variation` at a :ref:`Genotype` locus. +# variation: +# oneOf: +# - $ref: "#/$defs/Allele" +# - $ref: "#/$defs/Haplotype" +# description: >- +# A :ref:`MolecularVariation` at a :ref:`Genotype` locus. +# required: [ "count", "variation" ] # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Numerics, Comparators, and Ranges Range: - maturity: Alpha + maturity: draft description: An inclusive range of values bounded by one or more integers. type: array ordered: true @@ -526,7 +523,7 @@ $defs: minItems: 2 Residue: - maturity: Alpha + maturity: draft description: >- A character representing a specific residue (i.e., molecular species) or groupings of these ("ambiguity codes"), using `one-letter IUPAC @@ -536,7 +533,7 @@ $defs: pattern: '[A-Z*\-]' SequenceString: - maturity: Alpha + maturity: draft description: >- A character string of :ref:`Residues ` that represents a biological sequence using the conventional sequence order (5’-to-3’ for @@ -553,7 +550,7 @@ $defs: # ============================================================================= Adjacency: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: AJ keys: diff --git a/schema/vrs.json b/schema/vrs.json index 63ffb3b8..b73f2904 100644 --- a/schema/vrs.json +++ b/schema/vrs.json @@ -32,7 +32,7 @@ "Expression": { "type": "object", "privateTo": "Variation", - "maturity": "Alpha", + "maturity": "draft", "description": "Representation of a variation by a specified nomenclature or syntax for a Variation object. Common examples of expressions for the description of molecular variation include the HGVS and ISCN nomenclatures.", "properties": { "syntax": { @@ -94,7 +94,7 @@ } }, "Allele": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "prefix": "VA", "keys": [ @@ -176,7 +176,7 @@ "additionalProperties": false }, "Haplotype": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "prefix": "HT", "keys": [ @@ -251,7 +251,7 @@ "additionalProperties": false }, "CopyNumberCount": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "copies", @@ -330,7 +330,7 @@ "additionalProperties": false }, "CopyNumberChange": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "copyChange", @@ -490,7 +490,7 @@ "additionalProperties": false }, "SequenceLocation": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "end", @@ -571,7 +571,7 @@ "additionalProperties": false }, "SequenceReference": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "assigned": true }, @@ -640,7 +640,7 @@ } }, "ReferenceLengthExpression": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "length", @@ -709,7 +709,7 @@ "additionalProperties": false }, "LengthExpression": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "length", @@ -766,7 +766,7 @@ "additionalProperties": false }, "LiteralSequenceExpression": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "keys": [ "sequence", @@ -882,7 +882,7 @@ "additionalProperties": false }, "Range": { - "maturity": "Alpha", + "maturity": "draft", "description": "An inclusive range of values bounded by one or more integers.", "type": "array", "ordered": true, @@ -900,19 +900,19 @@ "minItems": 2 }, "Residue": { - "maturity": "Alpha", + "maturity": "draft", "description": "A character representing a specific residue (i.e., molecular species) or groupings of these (\"ambiguity codes\"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids.", "type": "string", "pattern": "[A-Z*\\-]" }, "SequenceString": { - "maturity": "Alpha", + "maturity": "draft", "description": "A character string of Residues that represents a biological sequence using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.", "type": "string", "pattern": "^[A-Z*\\-]*$" }, "Adjacency": { - "maturity": "Alpha", + "maturity": "draft", "ga4ghDigest": { "prefix": "AJ", "keys": [ diff --git a/schema/vrs.yaml b/schema/vrs.yaml index d445a6b0..122a23ed 100644 --- a/schema/vrs.yaml +++ b/schema/vrs.yaml @@ -16,7 +16,7 @@ $defs: Expression: type: object privateTo: Variation - maturity: Alpha + maturity: draft description: Representation of a variation by a specified nomenclature or syntax for a Variation object. Common examples of expressions for the description of molecular variation include the HGVS and ISCN nomenclatures. @@ -58,7 +58,7 @@ $defs: discriminator: propertyName: type Allele: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: VA keys: @@ -116,7 +116,7 @@ $defs: - state additionalProperties: false Haplotype: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: HT keys: @@ -179,7 +179,7 @@ $defs: - members additionalProperties: false CopyNumberCount: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - copies @@ -237,7 +237,7 @@ $defs: - location additionalProperties: false CopyNumberChange: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - copyChange @@ -369,7 +369,7 @@ $defs: - members additionalProperties: false SequenceLocation: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - end @@ -429,7 +429,7 @@ $defs: required: [] additionalProperties: false SequenceReference: - maturity: Alpha + maturity: draft ga4ghDigest: assigned: true type: object @@ -484,7 +484,7 @@ $defs: discriminator: propertyName: type ReferenceLengthExpression: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - length @@ -537,7 +537,7 @@ $defs: - type additionalProperties: false LengthExpression: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - length @@ -580,7 +580,7 @@ $defs: - type additionalProperties: false LiteralSequenceExpression: - maturity: Alpha + maturity: draft ga4ghDigest: keys: - sequence @@ -669,7 +669,7 @@ $defs: - variation additionalProperties: false Range: - maturity: Alpha + maturity: draft description: An inclusive range of values bounded by one or more integers. type: array ordered: true @@ -680,14 +680,14 @@ $defs: maxItems: 2 minItems: 2 Residue: - maturity: Alpha + maturity: draft description: A character representing a specific residue (i.e., molecular species) or groupings of these ("ambiguity codes"), using [one-letter IUPAC abbreviations](https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes) for nucleic acids and amino acids. type: string pattern: '[A-Z*\-]' SequenceString: - maturity: Alpha + maturity: draft description: "A character string of Residues that represents a biological sequence\ \ using the conventional sequence order (5\u2019-to-3\u2019 for nucleic acid\ \ sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity\ @@ -695,7 +695,7 @@ $defs: type: string pattern: ^[A-Z*\-]*$ Adjacency: - maturity: Alpha + maturity: draft ga4ghDigest: prefix: AJ keys: diff --git a/submodules/gks-common b/submodules/gks-common index 1b7e52d6..abe2f1ca 160000 --- a/submodules/gks-common +++ b/submodules/gks-common @@ -1 +1 @@ -Subproject commit 1b7e52d6013c6785300aa933efa9210e2aafa57b +Subproject commit abe2f1ca6b2d28ef286136ce00d5cc6e57934a1a From 0bdc41cef96b650cabb54f5bcab9e250f23d2f25 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Fri, 1 Mar 2024 18:08:27 -0500 Subject: [PATCH 2/3] rebuild artifacts --- schema/defs/vrs/Adjacency.rst | 8 +- schema/defs/vrs/Allele.rst | 8 +- schema/defs/vrs/CopyNumber.rst | 8 +- schema/defs/vrs/CopyNumberChange.rst | 8 +- schema/defs/vrs/CopyNumberCount.rst | 8 +- schema/defs/vrs/Ga4ghIdentifiableObject.rst | 10 +- schema/defs/vrs/Genotype.rst | 54 ----- schema/defs/vrs/GenotypeMember.rst | 46 ---- schema/defs/vrs/Haplotype.rst | 8 +- schema/defs/vrs/LengthExpression.rst | 4 - schema/defs/vrs/LiteralSequenceExpression.rst | 4 - schema/defs/vrs/ReferenceLengthExpression.rst | 4 - schema/defs/vrs/SequenceExpression.rst | 6 +- schema/defs/vrs/SequenceLocation.rst | 8 +- schema/defs/vrs/SequenceReference.rst | 6 +- schema/defs/vrs/ValueObject.rst | 37 +-- schema/defs/vrs/Variation.rst | 8 +- schema/merged.json | 228 +++--------------- schema/merged.yaml | 192 +++------------ schema/vrs.json | 228 +++--------------- schema/vrs.yaml | 192 +++------------ 21 files changed, 160 insertions(+), 915 deletions(-) delete mode 100644 schema/defs/vrs/Genotype.rst delete mode 100644 schema/defs/vrs/GenotypeMember.rst diff --git a/schema/defs/vrs/Adjacency.rst b/schema/defs/vrs/Adjacency.rst index 8b15d2ad..abca0626 100644 --- a/schema/defs/vrs/Adjacency.rst +++ b/schema/defs/vrs/Adjacency.rst @@ -32,14 +32,14 @@ Some Adjacency attributes are inherited from :ref:`Variation`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - MUST be "Adjacency". + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - expressions - :ref:`Expression` - 0..m diff --git a/schema/defs/vrs/Allele.rst b/schema/defs/vrs/Allele.rst index 94742635..088824df 100644 --- a/schema/defs/vrs/Allele.rst +++ b/schema/defs/vrs/Allele.rst @@ -32,14 +32,14 @@ Some Allele attributes are inherited from :ref:`Variation`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - MUST be "Allele" + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - expressions - :ref:`Expression` - 0..m diff --git a/schema/defs/vrs/CopyNumber.rst b/schema/defs/vrs/CopyNumber.rst index 8c3dc846..4ab6bcf1 100644 --- a/schema/defs/vrs/CopyNumber.rst +++ b/schema/defs/vrs/CopyNumber.rst @@ -32,14 +32,14 @@ Some CopyNumber attributes are inherited from :ref:`Variation`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - expressions - :ref:`Expression` - 0..m diff --git a/schema/defs/vrs/CopyNumberChange.rst b/schema/defs/vrs/CopyNumberChange.rst index ecf3ff47..dcc8849f 100644 --- a/schema/defs/vrs/CopyNumberChange.rst +++ b/schema/defs/vrs/CopyNumberChange.rst @@ -32,14 +32,14 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - MUST be "CopyNumberChange" + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - expressions - :ref:`Expression` - 0..m diff --git a/schema/defs/vrs/CopyNumberCount.rst b/schema/defs/vrs/CopyNumberCount.rst index 8265ed0c..d0392658 100644 --- a/schema/defs/vrs/CopyNumberCount.rst +++ b/schema/defs/vrs/CopyNumberCount.rst @@ -32,14 +32,14 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - MUST be "CopyNumberCount" + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - expressions - :ref:`Expression` - 0..m diff --git a/schema/defs/vrs/Ga4ghIdentifiableObject.rst b/schema/defs/vrs/Ga4ghIdentifiableObject.rst index b22abd48..267ba375 100644 --- a/schema/defs/vrs/Ga4ghIdentifiableObject.rst +++ b/schema/defs/vrs/Ga4ghIdentifiableObject.rst @@ -4,7 +4,7 @@ A contextual value object for which a GA4GH computed identifier can be created. **Information Model** -Some Ga4ghIdentifiableObject attributes are inherited from :ref:`ValueObject`. +Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core:Entity`. .. list-table:: :class: clean-wrap @@ -32,11 +32,11 @@ Some Ga4ghIdentifiableObject attributes are inherited from :ref:`ValueObject`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. diff --git a/schema/defs/vrs/Genotype.rst b/schema/defs/vrs/Genotype.rst deleted file mode 100644 index 2a3f9058..00000000 --- a/schema/defs/vrs/Genotype.rst +++ /dev/null @@ -1,54 +0,0 @@ -**Computational Definition** - -A quantified set of _in-trans_ :ref:`MolecularVariation` at a genomic locus. - - **Information Model** - -Some Genotype attributes are inherited from :ref:`Variation`. - - .. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - 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. 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 label for the entity. - * - description - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - `Extension `_ - - 0..m - - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - type - - string - - 0..1 - - MUST be "Genotype" - * - expressions - - :ref:`Expression` - - 0..m - - - * - members - - :ref:`GenotypeMember` - - 1..m - - Each GenotypeMember in `members` describes a :ref:`MolecularVariation` and the count of that variation at the locus. - * - count - - integer | :ref:`Range` - - 1..1 - - The total number of copies of all :ref:`MolecularVariation` at this locus, MUST be greater than or equal to the sum of :ref:`GenotypeMember` copy counts. If greater than the total counts, this implies additional :ref:`MolecularVariation` that are expected to exist but are not explicitly indicated. diff --git a/schema/defs/vrs/GenotypeMember.rst b/schema/defs/vrs/GenotypeMember.rst deleted file mode 100644 index 07ca5175..00000000 --- a/schema/defs/vrs/GenotypeMember.rst +++ /dev/null @@ -1,46 +0,0 @@ -**Computational Definition** - -A class for expressing the count of a specific :ref:`MolecularVariation` present _in-trans_ at a genomic locus represented by a :ref:`Genotype`. - - **Information Model** - -Some GenotypeMember attributes are inherited from :ref:`ValueObject`. - - .. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - 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. 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 label for the entity. - * - description - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - `Extension `_ - - 0..m - - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. - * - count - - :ref:`Range` | integer - - 1..1 - - The number of copies of the `variation` at a :ref:`Genotype` locus. - * - variation - - :ref:`Allele` | :ref:`Haplotype` - - 1..1 - - A :ref:`MolecularVariation` at a :ref:`Genotype` locus. diff --git a/schema/defs/vrs/Haplotype.rst b/schema/defs/vrs/Haplotype.rst index 78f88c78..7afd5f01 100644 --- a/schema/defs/vrs/Haplotype.rst +++ b/schema/defs/vrs/Haplotype.rst @@ -32,14 +32,14 @@ Some Haplotype attributes are inherited from :ref:`Variation`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - MUST be "Haplotype" + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - expressions - :ref:`Expression` - 0..m diff --git a/schema/defs/vrs/LengthExpression.rst b/schema/defs/vrs/LengthExpression.rst index 2541e2f7..0bf5539e 100644 --- a/schema/defs/vrs/LengthExpression.rst +++ b/schema/defs/vrs/LengthExpression.rst @@ -32,10 +32,6 @@ Some LengthExpression attributes are inherited from :ref:`SequenceExpression`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 1..1 diff --git a/schema/defs/vrs/LiteralSequenceExpression.rst b/schema/defs/vrs/LiteralSequenceExpression.rst index 65167c06..7941f4ff 100644 --- a/schema/defs/vrs/LiteralSequenceExpression.rst +++ b/schema/defs/vrs/LiteralSequenceExpression.rst @@ -32,10 +32,6 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 1..1 diff --git a/schema/defs/vrs/ReferenceLengthExpression.rst b/schema/defs/vrs/ReferenceLengthExpression.rst index 712026fa..4dc8d5af 100644 --- a/schema/defs/vrs/ReferenceLengthExpression.rst +++ b/schema/defs/vrs/ReferenceLengthExpression.rst @@ -32,10 +32,6 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 1..1 diff --git a/schema/defs/vrs/SequenceExpression.rst b/schema/defs/vrs/SequenceExpression.rst index 9a3bb11f..b7ac011c 100644 --- a/schema/defs/vrs/SequenceExpression.rst +++ b/schema/defs/vrs/SequenceExpression.rst @@ -4,7 +4,7 @@ An expression describing a :ref:`Sequence`. **Information Model** -Some SequenceExpression attributes are inherited from :ref:`ValueObject`. +Some SequenceExpression attributes are inherited from :ref:`gks.core:Entity`. .. list-table:: :class: clean-wrap @@ -32,10 +32,6 @@ Some SequenceExpression attributes are inherited from :ref:`ValueObject`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 1..1 diff --git a/schema/defs/vrs/SequenceLocation.rst b/schema/defs/vrs/SequenceLocation.rst index 87af6531..764be3dd 100644 --- a/schema/defs/vrs/SequenceLocation.rst +++ b/schema/defs/vrs/SequenceLocation.rst @@ -32,14 +32,14 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - MUST be "SequenceLocation" + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - sequenceReference - `IRI `_ | :ref:`SequenceReference` - 0..1 diff --git a/schema/defs/vrs/SequenceReference.rst b/schema/defs/vrs/SequenceReference.rst index e18c196e..a1bec2be 100644 --- a/schema/defs/vrs/SequenceReference.rst +++ b/schema/defs/vrs/SequenceReference.rst @@ -4,7 +4,7 @@ A sequence of nucleic or amino acid character codes. **Information Model** -Some SequenceReference attributes are inherited from :ref:`ValueObject`. +Some SequenceReference attributes are inherited from :ref:`gks.core:Entity`. .. list-table:: :class: clean-wrap @@ -32,10 +32,6 @@ Some SequenceReference attributes are inherited from :ref:`ValueObject`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 diff --git a/schema/defs/vrs/ValueObject.rst b/schema/defs/vrs/ValueObject.rst index 1b083c51..0f1de8be 100644 --- a/schema/defs/vrs/ValueObject.rst +++ b/schema/defs/vrs/ValueObject.rst @@ -1,38 +1,3 @@ **Computational Definition** -A contextual value whose equality is based on value, not identity. All VRS Value Objects may have computed digests from the VRS Computed Identifier algorithm. See https://en.wikipedia.org/wiki/Value_object for more on Value Objects. - - **Information Model** - -Some ValueObject attributes are inherited from :ref:`gks.core:Entity`. - - .. list-table:: - :class: clean-wrap - :header-rows: 1 - :align: left - :widths: auto - - * - Field - - Type - - Limits - - Description - * - 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. 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 label for the entity. - * - description - - string - - 0..1 - - A free-text description of the entity. - * - extensions - - `Extension `_ - - 0..m - - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. +A contextual value whose equality is based on value, not identity. See https://en.wikipedia.org/wiki/Value_object for more on Value Objects. diff --git a/schema/defs/vrs/Variation.rst b/schema/defs/vrs/Variation.rst index 26cd93d1..e5cb3b98 100644 --- a/schema/defs/vrs/Variation.rst +++ b/schema/defs/vrs/Variation.rst @@ -32,14 +32,14 @@ Some Variation attributes are inherited from :ref:`Ga4ghIdentifiableObject`. - `Extension `_ - 0..m - - * - digest - - string - - 0..1 - - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - type - string - 0..1 - + * - digest + - string + - 0..1 + - A sha512t24u digest created using the VRS Computed Identifier algorithm. * - expressions - :ref:`Expression` - 0..m diff --git a/schema/merged.json b/schema/merged.json index e7e03a0f..335f1211 100644 --- a/schema/merged.json +++ b/schema/merged.json @@ -18,9 +18,6 @@ { "$ref": "#/$defs/CopyNumberCount" }, - { - "$ref": "#/$defs/Genotype" - }, { "$ref": "#/$defs/Haplotype" } @@ -84,9 +81,6 @@ }, { "$ref": "#/$defs/CopyNumberCount" - }, - { - "$ref": "#/$defs/Genotype" } ], "discriminator": { @@ -125,17 +119,17 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "Allele", "default": "Allele", "description": "MUST be \"Allele\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -206,17 +200,17 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "Haplotype", "default": "Haplotype", "description": "MUST be \"Haplotype\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -282,17 +276,17 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "CopyNumberCount", "default": "CopyNumberCount", "description": "MUST be \"CopyNumberCount\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -361,17 +355,17 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "CopyNumberChange", "default": "CopyNumberChange", "description": "MUST be \"CopyNumberChange\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -411,84 +405,6 @@ ], "additionalProperties": false }, - "Genotype": { - "maturity": "Alpha", - "ga4ghDigest": { - "keys": [ - "count", - "members", - "type" - ], - "prefix": "GT" - }, - "description": "A quantified set of _in-trans_ MolecularVariation at a genomic locus.", - "type": "object", - "properties": { - "id": { - "type": "string", - "description": "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": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "#/$defs/Extension" - } - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "type": { - "type": "string", - "const": "Genotype", - "default": "Genotype", - "description": "MUST be \"Genotype\"" - }, - "expressions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "#/$defs/Expression" - } - }, - "members": { - "type": "array", - "ordered": false, - "uniqueItems": true, - "minItems": 1, - "items": { - "$ref": "#/$defs/GenotypeMember" - }, - "description": "Each GenotypeMember in `members` describes a MolecularVariation and the count of that variation at the locus." - }, - "count": { - "oneOf": [ - { - "$ref": "#/$defs/Range" - }, - { - "type": "integer" - } - ], - "description": "The total number of copies of all MolecularVariation at this locus, MUST be greater than or equal to the sum of GenotypeMember copy counts. If greater than the total counts, this implies additional MolecularVariation that are expected to exist but are not explicitly indicated." - } - }, - "required": [ - "count", - "members" - ], - "additionalProperties": false - }, "SequenceLocation": { "maturity": "draft", "ga4ghDigest": { @@ -522,17 +438,17 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "SequenceLocation", "default": "SequenceLocation", "description": "MUST be \"SequenceLocation\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "sequenceReference": { "oneOf": [ { @@ -597,11 +513,6 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "SequenceReference" @@ -670,11 +581,6 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "ReferenceLengthExpression", @@ -738,11 +644,6 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "LengthExpression", @@ -795,11 +696,6 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "LiteralSequenceExpression", @@ -817,70 +713,6 @@ ], "additionalProperties": false }, - "GenotypeMember": { - "privateTo": "Genotype", - "ga4ghDigest": { - "keys": [ - "count", - "variation" - ] - }, - "description": "A class for expressing the count of a specific MolecularVariation present _in-trans_ at a genomic locus represented by a Genotype.", - "type": "object", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "#/$defs/Extension" - } - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "count": { - "oneOf": [ - { - "$ref": "#/$defs/Range" - }, - { - "type": "integer" - } - ], - "description": "The number of copies of the `variation` at a Genotype locus." - }, - "variation": { - "oneOf": [ - { - "$ref": "#/$defs/Allele" - }, - { - "$ref": "#/$defs/Haplotype" - } - ], - "description": "A MolecularVariation at a Genotype locus." - } - }, - "required": [ - "count", - "variation" - ], - "additionalProperties": false - }, "Range": { "maturity": "draft", "description": "An inclusive range of values bounded by one or more integers.", @@ -943,17 +775,17 @@ "$ref": "#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "Adjacency", "default": "Adjacency", "description": "MUST be \"Adjacency\"." }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, diff --git a/schema/merged.yaml b/schema/merged.yaml index 7608fc1b..f0bb242b 100644 --- a/schema/merged.yaml +++ b/schema/merged.yaml @@ -9,7 +9,6 @@ $defs: - $ref: '#/$defs/Allele' - $ref: '#/$defs/CopyNumberChange' - $ref: '#/$defs/CopyNumberCount' - - $ref: '#/$defs/Genotype' - $ref: '#/$defs/Haplotype' discriminator: propertyName: type @@ -54,7 +53,6 @@ $defs: oneOf: - $ref: '#/$defs/CopyNumberChange' - $ref: '#/$defs/CopyNumberCount' - - $ref: '#/$defs/Genotype' discriminator: propertyName: type Allele: @@ -85,16 +83,16 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: Allele default: Allele description: MUST be "Allele" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -142,16 +140,16 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: Haplotype default: Haplotype description: MUST be "Haplotype" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -207,16 +205,16 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: CopyNumberCount default: CopyNumberCount description: MUST be "CopyNumberCount" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -265,16 +263,16 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: CopyNumberChange default: CopyNumberChange description: MUST be "CopyNumberChange" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -304,70 +302,6 @@ $defs: - copyChange - location additionalProperties: false - Genotype: - maturity: Alpha - ga4ghDigest: - keys: - - count - - members - - type - prefix: GT - description: A quantified set of _in-trans_ MolecularVariation at a genomic locus. - type: object - properties: - id: - type: string - description: 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: - type: string - description: A primary label for the entity. - description: - type: string - description: A free-text description of the entity. - extensions: - type: array - ordered: true - items: - $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ - type: - type: string - const: Genotype - default: Genotype - description: MUST be "Genotype" - expressions: - type: array - ordered: false - items: - $ref: '#/$defs/Expression' - members: - type: array - ordered: false - uniqueItems: true - minItems: 1 - items: - $ref: '#/$defs/GenotypeMember' - description: Each GenotypeMember in `members` describes a MolecularVariation - and the count of that variation at the locus. - count: - oneOf: - - $ref: '#/$defs/Range' - - type: integer - description: The total number of copies of all MolecularVariation at this - locus, MUST be greater than or equal to the sum of GenotypeMember copy counts. - If greater than the total counts, this implies additional MolecularVariation - that are expected to exist but are not explicitly indicated. - required: - - count - - members - additionalProperties: false SequenceLocation: maturity: draft ga4ghDigest: @@ -397,16 +331,16 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: SequenceLocation default: SequenceLocation description: MUST be "SequenceLocation" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ sequenceReference: oneOf: - $ref: '#/$defs/IRI' @@ -452,11 +386,6 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: SequenceReference @@ -510,11 +439,6 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: ReferenceLengthExpression @@ -562,11 +486,6 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: LengthExpression @@ -605,11 +524,6 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: LiteralSequenceExpression @@ -622,52 +536,6 @@ $defs: - sequence - type additionalProperties: false - GenotypeMember: - privateTo: Genotype - ga4ghDigest: - keys: - - count - - variation - description: A class for expressing the count of a specific MolecularVariation - present _in-trans_ at a genomic locus represented by a Genotype. - type: object - properties: - id: - type: string - description: 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: - type: string - description: A primary label for the entity. - description: - type: string - description: A free-text description of the entity. - extensions: - type: array - ordered: true - items: - $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ - count: - oneOf: - - $ref: '#/$defs/Range' - - type: integer - description: The number of copies of the `variation` at a Genotype locus. - variation: - oneOf: - - $ref: '#/$defs/Allele' - - $ref: '#/$defs/Haplotype' - description: A MolecularVariation at a Genotype locus. - required: - - count - - variation - additionalProperties: false Range: maturity: draft description: An inclusive range of values bounded by one or more integers. @@ -724,16 +592,16 @@ $defs: ordered: true items: $ref: '#/$defs/Extension' - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: Adjacency default: Adjacency description: MUST be "Adjacency". + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false diff --git a/schema/vrs.json b/schema/vrs.json index b73f2904..9473906b 100644 --- a/schema/vrs.json +++ b/schema/vrs.json @@ -18,9 +18,6 @@ { "$ref": "#/$defs/CopyNumberCount" }, - { - "$ref": "#/$defs/Genotype" - }, { "$ref": "#/$defs/Haplotype" } @@ -84,9 +81,6 @@ }, { "$ref": "#/$defs/CopyNumberCount" - }, - { - "$ref": "#/$defs/Genotype" } ], "discriminator": { @@ -125,17 +119,17 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "Allele", "default": "Allele", "description": "MUST be \"Allele\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -206,17 +200,17 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "Haplotype", "default": "Haplotype", "description": "MUST be \"Haplotype\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -282,17 +276,17 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "CopyNumberCount", "default": "CopyNumberCount", "description": "MUST be \"CopyNumberCount\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -361,17 +355,17 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "CopyNumberChange", "default": "CopyNumberChange", "description": "MUST be \"CopyNumberChange\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, @@ -411,84 +405,6 @@ ], "additionalProperties": false }, - "Genotype": { - "maturity": "Alpha", - "ga4ghDigest": { - "keys": [ - "count", - "members", - "type" - ], - "prefix": "GT" - }, - "description": "A quantified set of _in-trans_ MolecularVariation at a genomic locus.", - "type": "object", - "properties": { - "id": { - "type": "string", - "description": "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": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "gks.common.json#/$defs/Extension" - } - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "type": { - "type": "string", - "const": "Genotype", - "default": "Genotype", - "description": "MUST be \"Genotype\"" - }, - "expressions": { - "type": "array", - "ordered": false, - "items": { - "$ref": "#/$defs/Expression" - } - }, - "members": { - "type": "array", - "ordered": false, - "uniqueItems": true, - "minItems": 1, - "items": { - "$ref": "#/$defs/GenotypeMember" - }, - "description": "Each GenotypeMember in `members` describes a MolecularVariation and the count of that variation at the locus." - }, - "count": { - "oneOf": [ - { - "$ref": "#/$defs/Range" - }, - { - "type": "integer" - } - ], - "description": "The total number of copies of all MolecularVariation at this locus, MUST be greater than or equal to the sum of GenotypeMember copy counts. If greater than the total counts, this implies additional MolecularVariation that are expected to exist but are not explicitly indicated." - } - }, - "required": [ - "count", - "members" - ], - "additionalProperties": false - }, "SequenceLocation": { "maturity": "draft", "ga4ghDigest": { @@ -522,17 +438,17 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "SequenceLocation", "default": "SequenceLocation", "description": "MUST be \"SequenceLocation\"" }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "sequenceReference": { "oneOf": [ { @@ -597,11 +513,6 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "SequenceReference" @@ -670,11 +581,6 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "ReferenceLengthExpression", @@ -738,11 +644,6 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "LengthExpression", @@ -795,11 +696,6 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "LiteralSequenceExpression", @@ -817,70 +713,6 @@ ], "additionalProperties": false }, - "GenotypeMember": { - "privateTo": "Genotype", - "ga4ghDigest": { - "keys": [ - "count", - "variation" - ] - }, - "description": "A class for expressing the count of a specific MolecularVariation present _in-trans_ at a genomic locus represented by a Genotype.", - "type": "object", - "properties": { - "id": { - "type": "string", - "description": "The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE)." - }, - "label": { - "type": "string", - "description": "A primary label for the entity." - }, - "description": { - "type": "string", - "description": "A free-text description of the entity." - }, - "extensions": { - "type": "array", - "ordered": true, - "items": { - "$ref": "gks.common.json#/$defs/Extension" - } - }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, - "count": { - "oneOf": [ - { - "$ref": "#/$defs/Range" - }, - { - "type": "integer" - } - ], - "description": "The number of copies of the `variation` at a Genotype locus." - }, - "variation": { - "oneOf": [ - { - "$ref": "#/$defs/Allele" - }, - { - "$ref": "#/$defs/Haplotype" - } - ], - "description": "A MolecularVariation at a Genotype locus." - } - }, - "required": [ - "count", - "variation" - ], - "additionalProperties": false - }, "Range": { "maturity": "draft", "description": "An inclusive range of values bounded by one or more integers.", @@ -943,17 +775,17 @@ "$ref": "gks.common.json#/$defs/Extension" } }, - "digest": { - "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", - "type": "string", - "pattern": "^[0-9A-Za-z_\\-]{32}$" - }, "type": { "type": "string", "const": "Adjacency", "default": "Adjacency", "description": "MUST be \"Adjacency\"." }, + "digest": { + "description": "A sha512t24u digest created using the VRS Computed Identifier algorithm.", + "type": "string", + "pattern": "^[0-9A-Za-z_\\-]{32}$" + }, "expressions": { "type": "array", "ordered": false, diff --git a/schema/vrs.yaml b/schema/vrs.yaml index 122a23ed..bf19a7b2 100644 --- a/schema/vrs.yaml +++ b/schema/vrs.yaml @@ -9,7 +9,6 @@ $defs: - $ref: '#/$defs/Allele' - $ref: '#/$defs/CopyNumberChange' - $ref: '#/$defs/CopyNumberCount' - - $ref: '#/$defs/Genotype' - $ref: '#/$defs/Haplotype' discriminator: propertyName: type @@ -54,7 +53,6 @@ $defs: oneOf: - $ref: '#/$defs/CopyNumberChange' - $ref: '#/$defs/CopyNumberCount' - - $ref: '#/$defs/Genotype' discriminator: propertyName: type Allele: @@ -85,16 +83,16 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: Allele default: Allele description: MUST be "Allele" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -142,16 +140,16 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: Haplotype default: Haplotype description: MUST be "Haplotype" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -207,16 +205,16 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: CopyNumberCount default: CopyNumberCount description: MUST be "CopyNumberCount" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -265,16 +263,16 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: CopyNumberChange default: CopyNumberChange description: MUST be "CopyNumberChange" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false @@ -304,70 +302,6 @@ $defs: - copyChange - location additionalProperties: false - Genotype: - maturity: Alpha - ga4ghDigest: - keys: - - count - - members - - type - prefix: GT - description: A quantified set of _in-trans_ MolecularVariation at a genomic locus. - type: object - properties: - id: - type: string - description: 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: - type: string - description: A primary label for the entity. - description: - type: string - description: A free-text description of the entity. - extensions: - type: array - ordered: true - items: - $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ - type: - type: string - const: Genotype - default: Genotype - description: MUST be "Genotype" - expressions: - type: array - ordered: false - items: - $ref: '#/$defs/Expression' - members: - type: array - ordered: false - uniqueItems: true - minItems: 1 - items: - $ref: '#/$defs/GenotypeMember' - description: Each GenotypeMember in `members` describes a MolecularVariation - and the count of that variation at the locus. - count: - oneOf: - - $ref: '#/$defs/Range' - - type: integer - description: The total number of copies of all MolecularVariation at this - locus, MUST be greater than or equal to the sum of GenotypeMember copy counts. - If greater than the total counts, this implies additional MolecularVariation - that are expected to exist but are not explicitly indicated. - required: - - count - - members - additionalProperties: false SequenceLocation: maturity: draft ga4ghDigest: @@ -397,16 +331,16 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: SequenceLocation default: SequenceLocation description: MUST be "SequenceLocation" + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ sequenceReference: oneOf: - $ref: '#/$defs/SequenceReference' @@ -452,11 +386,6 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: SequenceReference @@ -510,11 +439,6 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: ReferenceLengthExpression @@ -562,11 +486,6 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: LengthExpression @@ -605,11 +524,6 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: LiteralSequenceExpression @@ -622,52 +536,6 @@ $defs: - sequence - type additionalProperties: false - GenotypeMember: - privateTo: Genotype - ga4ghDigest: - keys: - - count - - variation - description: A class for expressing the count of a specific MolecularVariation - present _in-trans_ at a genomic locus represented by a Genotype. - type: object - properties: - id: - type: string - description: 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: - type: string - description: A primary label for the entity. - description: - type: string - description: A free-text description of the entity. - extensions: - type: array - ordered: true - items: - $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ - count: - oneOf: - - $ref: '#/$defs/Range' - - type: integer - description: The number of copies of the `variation` at a Genotype locus. - variation: - oneOf: - - $ref: '#/$defs/Allele' - - $ref: '#/$defs/Haplotype' - description: A MolecularVariation at a Genotype locus. - required: - - count - - variation - additionalProperties: false Range: maturity: draft description: An inclusive range of values bounded by one or more integers. @@ -724,16 +592,16 @@ $defs: ordered: true items: $ref: gks.common.json#/$defs/Extension - digest: - description: A sha512t24u digest created using the VRS Computed Identifier - algorithm. - type: string - pattern: ^[0-9A-Za-z_\-]{32}$ type: type: string const: Adjacency default: Adjacency description: MUST be "Adjacency". + digest: + description: A sha512t24u digest created using the VRS Computed Identifier + algorithm. + type: string + pattern: ^[0-9A-Za-z_\-]{32}$ expressions: type: array ordered: false From 62271fe053be437d6238b42bd9d40f1a576fa5cf Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Fri, 1 Mar 2024 18:32:23 -0500 Subject: [PATCH 3/3] use new maturity model --- .requirements.txt | 2 +- submodules/gks-common | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.requirements.txt b/.requirements.txt index 1737e5de..00c92baf 100644 --- a/.requirements.txt +++ b/.requirements.txt @@ -3,6 +3,6 @@ python-jsonschema-objects>=0.4.0 jsonschema==3.2.0 ipython pyyaml -ga4gh.gks.metaschema==0.2.1 +ga4gh.gks.metaschema==0.3.0b1 sphinx ~= 7.2 sphinx-rtd-theme ~= 1.2 \ No newline at end of file diff --git a/submodules/gks-common b/submodules/gks-common index abe2f1ca..c19eb93f 160000 --- a/submodules/gks-common +++ b/submodules/gks-common @@ -1 +1 @@ -Subproject commit abe2f1ca6b2d28ef286136ce00d5cc6e57934a1a +Subproject commit c19eb93f320bea62484e83eefa8ed59bb637c4b7