Class: VariationDescriptor

URI: phenopackets:VariationDescriptor

erDiagram VariationDescriptor { stringList alternateLabels string description string id string label MoleculeContext moleculeContext string vrsRefAlleleSeq stringList xrefs } VcfRecord { string alt string chrom string filter string genomeAssembly string id string info integer pos string qual string ref } Variation { } VariationSet { } Text { string definition string id } Haplotype { } CopyNumber { string curie string id } Allele { string curie string id } OntologyClass { string id string label } GeneDescriptor { stringList alternateIds stringList alternateSymbols string description string symbol string valueId stringList xrefs } Extension { string name stringList value } Expression { string syntax string value string version } VariationDescriptor ||--|o OntologyClass : "allelicState" VariationDescriptor ||--}o Expression : "expressions" VariationDescriptor ||--}o Extension : "extensions" VariationDescriptor ||--|o GeneDescriptor : "geneContext" VariationDescriptor ||--|o OntologyClass : "structuralType" VariationDescriptor ||--|o Variation : "variation" VariationDescriptor ||--|o VcfRecord : "vcfRecord" Variation ||--|o Allele : "allele" Variation ||--|o CopyNumber : "copyNumber" Variation ||--|o Haplotype : "haplotype" Variation ||--|o Text : "text" Variation ||--|o VariationSet : "variationSet" CopyNumber ||--|o Allele : "allele" CopyNumber ||--|o DefiniteRange : "definiteRange" CopyNumber ||--|o DerivedSequenceExpression : "derivedSequenceExpression" CopyNumber ||--|o Gene : "gene" CopyNumber ||--|o Haplotype : "haplotype" CopyNumber ||--|o IndefiniteRange : "indefiniteRange" CopyNumber ||--|o LiteralSequenceExpression : "literalSequenceExpression" CopyNumber ||--|o Number : "number" CopyNumber ||--|o RepeatedSequenceExpression : "repeatedSequenceExpression" Allele ||--|o ChromosomeLocation : "chromosomeLocation" Allele ||--|o DerivedSequenceExpression : "derivedSequenceExpression" Allele ||--|o LiteralSequenceExpression : "literalSequenceExpression" Allele ||--|o RepeatedSequenceExpression : "repeatedSequenceExpression" Allele ||--|o SequenceLocation : "sequenceLocation"

Slots

Name	Cardinality and Range	Description	Inheritance
allelicState	0..1 OntologyClass	We RECOMMEND that the allelic_state of variant be described by terms from the...	direct
alternateLabels	0..* String	Common aliases for a variant, e	direct
description	0..1 String		direct
expressions	0..* Expression	HGVS, SPDI, and gnomAD-style strings should be represented as Expressions	direct
extensions	0..* Extension		direct
geneContext	0..1 GeneDescriptor	A specific gene context that applies to this variant	direct
id	0..1 String		direct
label	0..1 String		direct
moleculeContext	0..1 MoleculeContext	The molecular context of the vrs variation	direct
structuralType	0..1 OntologyClass	The structural variant type associated with this variant, such as a substitut...	direct
variation	0..1 Variation		direct
vcfRecord	0..1 VcfRecord	A VCF Record of the variant	direct
vrsRefAlleleSeq	0..1 String	A Sequence corresponding to a “ref allele”, describing the sequence expected ...	direct
xrefs	0..* String	Allele registry, ClinVar, or other related IDs should be included as xrefs	direct

Usages

used by	used in	type	used
VariantInterpretation	variationDescriptor	range	VariationDescriptor

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/linkml/phenopackets/phenopackets

Mappings

Mapping Type	Mapped Value
self	phenopackets:VariationDescriptor
native	phenopackets:VariationDescriptor

LinkML Source

Direct

name: VariationDescriptor
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  allelicState:
    name: allelicState
    annotations:
      rank:
        tag: rank
        value: 14
    description: We RECOMMEND that the allelic_state of variant be described by terms
      from the Genotype Ontology (GENO). These SHOULD descend from concept GENO:0000875.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - VariationDescriptor
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  alternateLabels:
    name: alternateLabels
    annotations:
      rank:
        tag: rank
        value: 9
    description: Common aliases for a variant, e.g. EGFR vIII, are alternate labels
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - VariationDescriptor
    range: string
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  expressions:
    name: expressions
    annotations:
      rank:
        tag: rank
        value: 6
    description: HGVS, SPDI, and gnomAD-style strings should be represented as Expressions
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - VariationDescriptor
    range: Expression
    inlined: true
    inlined_as_list: true
  extensions:
    name: extensions
    annotations:
      rank:
        tag: rank
        value: 10
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    domain_of:
    - VariationDescriptor
    range: Extension
    inlined: true
    inlined_as_list: true
  geneContext:
    name: geneContext
    annotations:
      rank:
        tag: rank
        value: 5
    description: A specific gene context that applies to this variant.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - VariationDescriptor
    range: GeneDescriptor
    inlined: true
    inlined_as_list: true
  id:
    name: id
    annotations:
      percent_encoded:
        tag: percent_encoded
        value: true
      rank:
        tag: rank
        value: 1
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  label:
    name: label
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - OntologyClass
    - VariationDescriptor
    range: string
  moleculeContext:
    name: moleculeContext
    annotations:
      rank:
        tag: rank
        value: 11
    description: The molecular context of the vrs variation. Must be one of “genomic”,
      “transcript”, or “protein”. Defaults to "unspecified_molecule_context"
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - VariationDescriptor
    range: MoleculeContext
  structuralType:
    name: structuralType
    annotations:
      rank:
        tag: rank
        value: 12
    description: The structural variant type associated with this variant, such as
      a substitution, deletion, or fusion. We RECOMMEND using a descendent term of
      SO:0001537.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - VariationDescriptor
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  variation:
    name: variation
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - VariationDescriptor
    range: Variation
  vcfRecord:
    name: vcfRecord
    annotations:
      rank:
        tag: rank
        value: 7
    description: A VCF Record of the variant. This SHOULD be a single allele, the
      VCF genotype (GT) field should be represented in the allelic_state
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - VariationDescriptor
    range: VcfRecord
  vrsRefAlleleSeq:
    name: vrsRefAlleleSeq
    annotations:
      rank:
        tag: rank
        value: 13
    description: A Sequence corresponding to a “ref allele”, describing the sequence
      expected at a SequenceLocation reference.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - VariationDescriptor
    range: string
  xrefs:
    name: xrefs
    annotations:
      rank:
        tag: rank
        value: 8
    description: Allele registry, ClinVar, or other related IDs should be included
      as xrefs
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    domain_of:
    - GeneDescriptor
    - VariationDescriptor
    range: string

Induced

name: VariationDescriptor
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  allelicState:
    name: allelicState
    annotations:
      rank:
        tag: rank
        value: 14
    description: We RECOMMEND that the allelic_state of variant be described by terms
      from the Genotype Ontology (GENO). These SHOULD descend from concept GENO:0000875.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: allelicState
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  alternateLabels:
    name: alternateLabels
    annotations:
      rank:
        tag: rank
        value: 9
    description: Common aliases for a variant, e.g. EGFR vIII, are alternate labels
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: alternateLabels
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: string
  description:
    name: description
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: description
    owner: VariationDescriptor
    domain_of:
    - Cohort
    - ExternalReference
    - Measurement
    - PhenotypicFeature
    - Biosample
    - GeneDescriptor
    - VariationDescriptor
    range: string
  expressions:
    name: expressions
    annotations:
      rank:
        tag: rank
        value: 6
    description: HGVS, SPDI, and gnomAD-style strings should be represented as Expressions
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: expressions
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: Expression
    inlined: true
    inlined_as_list: true
  extensions:
    name: extensions
    annotations:
      rank:
        tag: rank
        value: 10
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    multivalued: true
    alias: extensions
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: Extension
    inlined: true
    inlined_as_list: true
  geneContext:
    name: geneContext
    annotations:
      rank:
        tag: rank
        value: 5
    description: A specific gene context that applies to this variant.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: geneContext
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: GeneDescriptor
    inlined: true
    inlined_as_list: true
  id:
    name: id
    annotations:
      percent_encoded:
        tag: percent_encoded
        value: true
      rank:
        tag: rank
        value: 1
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: id
    owner: VariationDescriptor
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  label:
    name: label
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: label
    owner: VariationDescriptor
    domain_of:
    - OntologyClass
    - VariationDescriptor
    range: string
  moleculeContext:
    name: moleculeContext
    annotations:
      rank:
        tag: rank
        value: 11
    description: The molecular context of the vrs variation. Must be one of “genomic”,
      “transcript”, or “protein”. Defaults to "unspecified_molecule_context"
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: moleculeContext
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: MoleculeContext
  structuralType:
    name: structuralType
    annotations:
      rank:
        tag: rank
        value: 12
    description: The structural variant type associated with this variant, such as
      a substitution, deletion, or fusion. We RECOMMEND using a descendent term of
      SO:0001537.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: structuralType
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: OntologyClass
    inlined: true
    inlined_as_list: true
  variation:
    name: variation
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: variation
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: Variation
  vcfRecord:
    name: vcfRecord
    annotations:
      rank:
        tag: rank
        value: 7
    description: A VCF Record of the variant. This SHOULD be a single allele, the
      VCF genotype (GT) field should be represented in the allelic_state
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: vcfRecord
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: VcfRecord
  vrsRefAlleleSeq:
    name: vrsRefAlleleSeq
    annotations:
      rank:
        tag: rank
        value: 13
    description: A Sequence corresponding to a “ref allele”, describing the sequence
      expected at a SequenceLocation reference.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: vrsRefAlleleSeq
    owner: VariationDescriptor
    domain_of:
    - VariationDescriptor
    range: string
  xrefs:
    name: xrefs
    annotations:
      rank:
        tag: rank
        value: 8
    description: Allele registry, ClinVar, or other related IDs should be included
      as xrefs
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    multivalued: true
    alias: xrefs
    owner: VariationDescriptor
    domain_of:
    - GeneDescriptor
    - VariationDescriptor
    range: string