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Class: Variation

URI: phenopackets:Variation

erDiagram Variation { } VariationSet { } Text { string definition string id } Haplotype { } CopyNumber { string curie string id } RepeatedSequenceExpression { } Number { integer value } LiteralSequenceExpression { string sequence } IndefiniteRange { string comparator integer value } Gene { string geneId } DerivedSequenceExpression { boolean reverseComplement } DefiniteRange { integer max integer min } Allele { string curie string id } 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" RepeatedSequenceExpression ||--|o DefiniteRange : "definiteRange" RepeatedSequenceExpression ||--|o DerivedSequenceExpression : "derivedSequenceExpression" RepeatedSequenceExpression ||--|o IndefiniteRange : "indefiniteRange" RepeatedSequenceExpression ||--|o LiteralSequenceExpression : "literalSequenceExpression" RepeatedSequenceExpression ||--|o Number : "number" DerivedSequenceExpression ||--|o SequenceLocation : "location" 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
allele 0..1
Allele		 direct
copyNumber 0..1
CopyNumber		 direct
haplotype 0..1
Haplotype		 direct
text 0..1
Text		 direct
variationSet 0..1
VariationSet		 direct

Usages

used by used in type used
VariationDescriptor variation range Variation

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Variation
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  allele:
    name: allele
    annotations:
      rank:
        tag: rank
        value: 1
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Allele
  copyNumber:
    name: copyNumber
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Abundance
    - Member
    - SystemicVariation
    - Variation
    range: CopyNumber
  haplotype:
    name: haplotype
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Haplotype
  text:
    name: text
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Member
    - UtilityVariation
    - Variation
    range: Text
  variationSet:
    name: variationSet
    annotations:
      rank:
        tag: rank
        value: 5
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Member
    - UtilityVariation
    - Variation
    range: VariationSet
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        allele:
          name: allele
          required: true
    - slot_conditions:
        haplotype:
          name: haplotype
          required: true
    - slot_conditions:
        copyNumber:
          name: copyNumber
          required: true
    - slot_conditions:
        text:
          name: text
          required: true
    - slot_conditions:
        variationSet:
          name: variationSet
          required: true

Induced

name: Variation
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  allele:
    name: allele
    annotations:
      rank:
        tag: rank
        value: 1
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: allele
    owner: Variation
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Allele
  copyNumber:
    name: copyNumber
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: copyNumber
    owner: Variation
    domain_of:
    - Abundance
    - Member
    - SystemicVariation
    - Variation
    range: CopyNumber
  haplotype:
    name: haplotype
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: haplotype
    owner: Variation
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Haplotype
  text:
    name: text
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: text
    owner: Variation
    domain_of:
    - Member
    - UtilityVariation
    - Variation
    range: Text
  variationSet:
    name: variationSet
    annotations:
      rank:
        tag: rank
        value: 5
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: variationSet
    owner: Variation
    domain_of:
    - Member
    - UtilityVariation
    - Variation
    range: VariationSet
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        allele:
          name: allele
          required: true
    - slot_conditions:
        haplotype:
          name: haplotype
          required: true
    - slot_conditions:
        copyNumber:
          name: copyNumber
          required: true
    - slot_conditions:
        text:
          name: text
          required: true
    - slot_conditions:
        variationSet:
          name: variationSet
          required: true