Class: GenomicInterpretation

A statement about the contribution of a genomic element towards the observed phenotype. Note that this does not intend to encode any knowledge or results of specific computations.

URI: phenopackets:GenomicInterpretation

erDiagram GenomicInterpretation { InterpretationStatus interpretationStatus string subjectOrBiosampleId } VariantInterpretation { AcmgPathogenicityClassification acmgPathogenicityClassification TherapeuticActionability therapeuticActionability } VariationDescriptor { stringList alternateLabels string description string id string label MoleculeContext moleculeContext string vrsRefAlleleSeq stringList xrefs } GeneDescriptor { stringList alternateIds stringList alternateSymbols string description string symbol string valueId stringList xrefs } GenomicInterpretation ||--|o GeneDescriptor : "gene" GenomicInterpretation ||--|o VariantInterpretation : "variantInterpretation" VariantInterpretation ||--|o VariationDescriptor : "variationDescriptor" 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"

Slots

Name	Cardinality and Range	Description	Inheritance
gene	0..1 GeneDescriptor		direct
interpretationStatus	0..1 InterpretationStatus		direct
subjectOrBiosampleId	0..1 String	identifier for the subject of the interpretation	direct
variantInterpretation	0..1 VariantInterpretation		direct

Usages

used by	used in	type	used
Diagnosis	genomicInterpretations	range	GenomicInterpretation

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GenomicInterpretation
description: A statement about the contribution of a genomic element towards the observed
  phenotype. Note that this does not intend to encode any knowledge or results of
  specific computations.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  gene:
    name: gene
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    domain_of:
    - CopyNumber
    - Feature
    - GenomicInterpretation
    range: GeneDescriptor
    inlined: true
    inlined_as_list: true
  interpretationStatus:
    name: interpretationStatus
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - GenomicInterpretation
    range: InterpretationStatus
  subjectOrBiosampleId:
    name: subjectOrBiosampleId
    annotations:
      rank:
        tag: rank
        value: 1
    description: identifier for the subject of the interpretation. This MUST be the
      individual id or a biosample id of the enclosing phenopacket.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - GenomicInterpretation
    range: string
  variantInterpretation:
    name: variantInterpretation
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    domain_of:
    - GenomicInterpretation
    range: VariantInterpretation
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        gene:
          name: gene
          required: true
    - slot_conditions:
        variantInterpretation:
          name: variantInterpretation
          required: true

Induced

name: GenomicInterpretation
description: A statement about the contribution of a genomic element towards the observed
  phenotype. Note that this does not intend to encode any knowledge or results of
  specific computations.
from_schema: https://w3id.org/linkml/phenopackets/phenopackets
attributes:
  gene:
    name: gene
    annotations:
      rank:
        tag: rank
        value: 3
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    alias: gene
    owner: GenomicInterpretation
    domain_of:
    - CopyNumber
    - Feature
    - GenomicInterpretation
    range: GeneDescriptor
    inlined: true
    inlined_as_list: true
  interpretationStatus:
    name: interpretationStatus
    annotations:
      rank:
        tag: rank
        value: 2
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: interpretationStatus
    owner: GenomicInterpretation
    domain_of:
    - GenomicInterpretation
    range: InterpretationStatus
  subjectOrBiosampleId:
    name: subjectOrBiosampleId
    annotations:
      rank:
        tag: rank
        value: 1
    description: identifier for the subject of the interpretation. This MUST be the
      individual id or a biosample id of the enclosing phenopacket.
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: subjectOrBiosampleId
    owner: GenomicInterpretation
    domain_of:
    - GenomicInterpretation
    range: string
  variantInterpretation:
    name: variantInterpretation
    annotations:
      rank:
        tag: rank
        value: 4
    description: ''
    from_schema: https://w3id.org/linkml/phenopackets/phenopackets
    rank: 1000
    alias: variantInterpretation
    owner: GenomicInterpretation
    domain_of:
    - GenomicInterpretation
    range: VariantInterpretation
rules:
- postconditions:
    exactly_one_of:
    - slot_conditions:
        gene:
          name: gene
          required: true
    - slot_conditions:
        variantInterpretation:
          name: variantInterpretation
          required: true