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Class: VariantToEntityAssociationMixin

classDiagram class VariantToEntityAssociationMixin VariantToEntityAssociationMixin <|-- VariantToGeneAssociation VariantToEntityAssociationMixin <|-- VariantToPopulationAssociation VariantToEntityAssociationMixin <|-- VariantToPhenotypicFeatureAssociation VariantToEntityAssociationMixin <|-- VariantToDiseaseAssociation VariantToEntityAssociationMixin : object VariantToEntityAssociationMixin --|> NamedThing : object VariantToEntityAssociationMixin : predicate VariantToEntityAssociationMixin : subject VariantToEntityAssociationMixin --|> SequenceVariant : subject

Slots

Name Cardinality and Range Inheritance Examples
subject:
a sequence variant in which the allele state is associated with some other entity 		1
SequenceVariant		 direct CLINVAR:38077, ClinGen:CA024716
predicate:
Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats 		1
Uriorcurie		 direct
object:
connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. 		1
NamedThing		 direct

Mixin Usage

mixed into description
VariantToGeneAssociation An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)
VariantToPopulationAssociation An association between a variant and a population, where the variant has particular frequency in the population
VariantToPhenotypicFeatureAssociation An association between a sequence variant and a phenotypic feature, in which the allele state of the variant is linked to the manifestation of the phenotype.
VariantToDiseaseAssociation An association between a sequence variant and a disease, in which the allele state of the variant is linked to the disease state.

LinkML Source

name: variant to entity association mixin
local_names:
  ga4gh:
    local_name_source: ga4gh
    local_name_value: variant annotation
from_schema: https://w3id.org/biolink/vocab/
mixin: true
slots:
- subject
- predicate
- object
slot_usage:
  subject:
    name: subject
    description: a sequence variant in which the allele state is associated with some
      other entity
    examples:
    - value: CLINVAR:38077
      description: CLINVAR representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)
    - value: ClinGen:CA024716
      description: chr13:g.32921033G>C (hg19) in ClinGen
    range: sequence variant
defining_slots:
- subject