Class: CopyNumber

URI: phenopackets:CopyNumber

erDiagram CopyNumber { string curie string id } RepeatedSequenceExpression { } Number { integer value } LiteralSequenceExpression { string sequence } IndefiniteRange { string comparator integer value } DerivedSequenceExpression { boolean reverseComplement } DefiniteRange { integer max integer min } Haplotype { } Gene { string geneId } Allele { string curie string id } SequenceLocation { string id string sequenceId } ChromosomeLocation { string chr string id string speciesId } 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" SequenceLocation ||--|o SequenceInterval : "sequenceInterval" ChromosomeLocation ||--|o CytobandInterval : "interval"

Slots

Name	Cardinality and Range	Inheritance
allele	0..1 Allele	direct
curie	0..1 String	direct
definiteRange	0..1 DefiniteRange	direct
derivedSequenceExpression	0..1 DerivedSequenceExpression	direct
gene	0..1 Gene	direct
haplotype	0..1 Haplotype	direct
id	0..1 String	direct
indefiniteRange	0..1 IndefiniteRange	direct
literalSequenceExpression	0..1 LiteralSequenceExpression	direct
number	0..1 Number	direct
repeatedSequenceExpression	0..1 RepeatedSequenceExpression	direct

Usages

used by	used in	type	used
Abundance	copyNumber	range	CopyNumber
Member	copyNumber	range	CopyNumber
SystemicVariation	copyNumber	range	CopyNumber
Variation	copyNumber	range	CopyNumber

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: CopyNumber
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  allele:
    name: allele
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Allele
  curie:
    name: curie
    annotations:
      rank:
        tag: rank
        value: 8
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Allele
    - CopyNumber
    - Member
    range: string
  definiteRange:
    name: definiteRange
    annotations:
      rank:
        tag: rank
        value: 11
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - CopyNumber
    - RepeatedSequenceExpression
    range: DefiniteRange
  derivedSequenceExpression:
    name: derivedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 6
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: DerivedSequenceExpression
  gene:
    name: gene
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - CopyNumber
    - Feature
    - GenomicInterpretation
    range: Gene
  haplotype:
    name: haplotype
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Haplotype
  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
  indefiniteRange:
    name: indefiniteRange
    annotations:
      rank:
        tag: rank
        value: 10
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - CopyNumber
    - RepeatedSequenceExpression
    range: IndefiniteRange
  literalSequenceExpression:
    name: literalSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 5
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: LiteralSequenceExpression
  number:
    name: number
    annotations:
      rank:
        tag: rank
        value: 9
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - CopyNumber
    - RepeatedSequenceExpression
    range: Number
  repeatedSequenceExpression:
    name: repeatedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 7
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - Allele
    - CopyNumber
    - SequenceExpression
    range: RepeatedSequenceExpression
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        number:
          name: number
          required: true
    - slot_conditions:
        indefiniteRange:
          name: indefiniteRange
          required: true
    - slot_conditions:
        definiteRange:
          name: definiteRange
          required: true

Induced

name: CopyNumber
description: ''
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  allele:
    name: allele
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: allele
    owner: CopyNumber
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Allele
  curie:
    name: curie
    annotations:
      rank:
        tag: rank
        value: 8
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: curie
    owner: CopyNumber
    domain_of:
    - Allele
    - CopyNumber
    - Member
    range: string
  definiteRange:
    name: definiteRange
    annotations:
      rank:
        tag: rank
        value: 11
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: definiteRange
    owner: CopyNumber
    domain_of:
    - CopyNumber
    - RepeatedSequenceExpression
    range: DefiniteRange
  derivedSequenceExpression:
    name: derivedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 6
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: derivedSequenceExpression
    owner: CopyNumber
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: DerivedSequenceExpression
  gene:
    name: gene
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: gene
    owner: CopyNumber
    domain_of:
    - CopyNumber
    - Feature
    - GenomicInterpretation
    range: Gene
  haplotype:
    name: haplotype
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: haplotype
    owner: CopyNumber
    domain_of:
    - CopyNumber
    - Member
    - MolecularVariation
    - Variation
    range: Haplotype
  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: CopyNumber
    domain_of:
    - Cohort
    - Family
    - Phenopacket
    - ExternalReference
    - OntologyClass
    - Biosample
    - Allele
    - ChromosomeLocation
    - CopyNumber
    - Member
    - SequenceLocation
    - Text
    - VariationDescriptor
    - VcfRecord
    - Interpretation
    - Individual
    - Resource
    range: string
  indefiniteRange:
    name: indefiniteRange
    annotations:
      rank:
        tag: rank
        value: 10
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: indefiniteRange
    owner: CopyNumber
    domain_of:
    - CopyNumber
    - RepeatedSequenceExpression
    range: IndefiniteRange
  literalSequenceExpression:
    name: literalSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 5
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: literalSequenceExpression
    owner: CopyNumber
    domain_of:
    - Allele
    - CopyNumber
    - RepeatedSequenceExpression
    - SequenceExpression
    range: LiteralSequenceExpression
  number:
    name: number
    annotations:
      rank:
        tag: rank
        value: 9
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: number
    owner: CopyNumber
    domain_of:
    - CopyNumber
    - RepeatedSequenceExpression
    range: Number
  repeatedSequenceExpression:
    name: repeatedSequenceExpression
    annotations:
      rank:
        tag: rank
        value: 7
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: repeatedSequenceExpression
    owner: CopyNumber
    domain_of:
    - Allele
    - CopyNumber
    - SequenceExpression
    range: RepeatedSequenceExpression
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        number:
          name: number
          required: true
    - slot_conditions:
        indefiniteRange:
          name: indefiniteRange
          required: true
    - slot_conditions:
        definiteRange:
          name: definiteRange
          required: true