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Class: Allele

URI: phenopackets:Allele

erDiagram Allele { string curie string id } SequenceLocation { string id string sequenceId } SequenceInterval { } RepeatedSequenceExpression { } Number { integer value } LiteralSequenceExpression { string sequence } IndefiniteRange { string comparator integer value } DerivedSequenceExpression { boolean reverseComplement } DefiniteRange { integer max integer min } ChromosomeLocation { string chr string id string speciesId } CytobandInterval { string end string start } Allele ||--|o ChromosomeLocation : "chromosomeLocation" Allele ||--|o DerivedSequenceExpression : "derivedSequenceExpression" Allele ||--|o LiteralSequenceExpression : "literalSequenceExpression" Allele ||--|o RepeatedSequenceExpression : "repeatedSequenceExpression" Allele ||--|o SequenceLocation : "sequenceLocation" SequenceLocation ||--|o SequenceInterval : "sequenceInterval" SequenceInterval ||--|o DefiniteRange : "endDefiniteRange" SequenceInterval ||--|o IndefiniteRange : "endIndefiniteRange" SequenceInterval ||--|o Number : "endNumber" SequenceInterval ||--|o DefiniteRange : "startDefiniteRange" SequenceInterval ||--|o IndefiniteRange : "startIndefiniteRange" SequenceInterval ||--|o Number : "startNumber" RepeatedSequenceExpression ||--|o DefiniteRange : "definiteRange" RepeatedSequenceExpression ||--|o DerivedSequenceExpression : "derivedSequenceExpression" RepeatedSequenceExpression ||--|o IndefiniteRange : "indefiniteRange" RepeatedSequenceExpression ||--|o LiteralSequenceExpression : "literalSequenceExpression" RepeatedSequenceExpression ||--|o Number : "number" DerivedSequenceExpression ||--|o SequenceLocation : "location" ChromosomeLocation ||--|o CytobandInterval : "interval"

Slots

Name Cardinality and Range Description Inheritance
chromosomeLocation 0..1
ChromosomeLocation		 direct
curie 0..1
String		 direct
derivedSequenceExpression 0..1
DerivedSequenceExpression		 direct
id 0..1
String		 direct
literalSequenceExpression 0..1
LiteralSequenceExpression		 direct
repeatedSequenceExpression 0..1
RepeatedSequenceExpression		 direct
sequenceLocation 0..1
SequenceLocation		 direct

Usages

used by used in type used
CopyNumber allele range Allele
Member allele range Allele
MolecularVariation allele range Allele
Variation allele range Allele

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Allele
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  chromosomeLocation:
    name: chromosomeLocation
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Allele
    - Location
    range: ChromosomeLocation
  curie:
    name: curie
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Allele
    - CopyNumber
    - Member
    range: string
  derivedSequenceExpression:
    name: derivedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 6
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: DerivedSequenceExpression
  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
  literalSequenceExpression:
    name: literalSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 5
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: LiteralSequenceExpression
  repeatedSequenceExpression:
    name: repeatedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 7
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Allele
    - CopyNumber
    - SequenceExpression
    range: RepeatedSequenceExpression
  sequenceLocation:
    name: sequenceLocation
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - Allele
    - Location
    range: SequenceLocation
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        literalSequenceExpression:
          name: literalSequenceExpression
          required: true
    - slot_conditions:
        derivedSequenceExpression:
          name: derivedSequenceExpression
          required: true
    - slot_conditions:
        repeatedSequenceExpression:
          name: repeatedSequenceExpression
          required: true

Induced

name: Allele
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  chromosomeLocation:
    name: chromosomeLocation
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: chromosomeLocation
    owner: Allele
    domain_of:
    - Allele
    - Location
    range: ChromosomeLocation
  curie:
    name: curie
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: curie
    owner: Allele
    domain_of:
    - Allele
    - CopyNumber
    - Member
    range: string
  derivedSequenceExpression:
    name: derivedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 6
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: derivedSequenceExpression
    owner: Allele
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: DerivedSequenceExpression
  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: Allele
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  literalSequenceExpression:
    name: literalSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 5
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: literalSequenceExpression
    owner: Allele
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: LiteralSequenceExpression
  repeatedSequenceExpression:
    name: repeatedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 7
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: repeatedSequenceExpression
    owner: Allele
    domain_of:
    - Allele
    - CopyNumber
    - SequenceExpression
    range: RepeatedSequenceExpression
  sequenceLocation:
    name: sequenceLocation
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: sequenceLocation
    owner: Allele
    domain_of:
    - Allele
    - Location
    range: SequenceLocation
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        literalSequenceExpression:
          name: literalSequenceExpression
          required: true
    - slot_conditions:
        derivedSequenceExpression:
          name: derivedSequenceExpression
          required: true
    - slot_conditions:
        repeatedSequenceExpression:
          name: repeatedSequenceExpression
          required: true