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Class: 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)

URI: biolink:VariantToGeneAssociation

classDiagram class VariantToGeneAssociation VariantToEntityAssociationMixin <|-- VariantToGeneAssociation Association <|-- VariantToGeneAssociation VariantToGeneAssociation <|-- VariantToGeneExpressionAssociation VariantToGeneAssociation : aggregator_knowledge_source VariantToGeneAssociation : category VariantToGeneAssociation : description VariantToGeneAssociation : has_attribute VariantToGeneAssociation --|> attribute : has_attribute VariantToGeneAssociation : has_evidence VariantToGeneAssociation --|> evidence type : has_evidence VariantToGeneAssociation : id VariantToGeneAssociation : iri VariantToGeneAssociation : knowledge_source VariantToGeneAssociation : name VariantToGeneAssociation : negated VariantToGeneAssociation : object VariantToGeneAssociation --|> gene : object VariantToGeneAssociation : object_category VariantToGeneAssociation --|> ontology class : object_category VariantToGeneAssociation : object_category_closure VariantToGeneAssociation --|> ontology class : object_category_closure VariantToGeneAssociation : object_closure VariantToGeneAssociation : object_label_closure VariantToGeneAssociation : object_namespace VariantToGeneAssociation : original_object VariantToGeneAssociation : original_predicate VariantToGeneAssociation : original_subject VariantToGeneAssociation : predicate VariantToGeneAssociation : primary_knowledge_source VariantToGeneAssociation : publications VariantToGeneAssociation --|> publication : publications VariantToGeneAssociation : qualifiers VariantToGeneAssociation --|> ontology class : qualifiers VariantToGeneAssociation : retrieval_source_ids VariantToGeneAssociation --|> retrieval source : retrieval_source_ids VariantToGeneAssociation : subject VariantToGeneAssociation --|> sequence variant : subject VariantToGeneAssociation : subject_category VariantToGeneAssociation --|> ontology class : subject_category VariantToGeneAssociation : subject_category_closure VariantToGeneAssociation --|> ontology class : subject_category_closure VariantToGeneAssociation : subject_closure VariantToGeneAssociation : subject_label_closure VariantToGeneAssociation : subject_namespace VariantToGeneAssociation : timepoint VariantToGeneAssociation : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subject 1..1
SequenceVariant		 a sequence variant in which the allele state is associated with some other en... Association
predicate 1..1
PredicateType		 A high-level grouping for the relationship type Association
object 1..1
Gene		 connects an association to the object of the association Association
negated 0..1
Boolean		 if set to true, then the association is negated i Association
qualifiers 0..*
OntologyClass		 connects an association to qualifiers that modify or qualify the meaning of t... Association
publications 0..*
Publication		 One or more publications that report the statement expressed in an Associati... Association
has_evidence 0..*
EvidenceType		 connects an association to an instance of supporting evidence Association
knowledge_source 0..1
String		 An Information Resource from which the knowledge expressed in an Association ... Association
primary_knowledge_source 0..1
String		 The most upstream source of the knowledge expressed in an Association that an... Association
aggregator_knowledge_source 0..*
String		 An intermediate aggregator resource from which knowledge expressed in an Asso... Association
timepoint 0..1
TimeType		 a point in time Association
original_subject 0..1
String		 used to hold the original subject of a relation (or predicate) that an extern... Association
original_predicate 0..1
Uriorcurie		 used to hold the original relation/predicate that an external knowledge sourc... Association
original_object 0..1
String		 used to hold the original object of a relation (or predicate) that an externa... Association
subject_category 0..1
OntologyClass		 Used to hold the biolink class/category of an association Association
object_category 0..1
OntologyClass		 Used to hold the biolink class/category of an association Association
subject_closure 0..*
String		 Used to hold the subject closure of an association Association
object_closure 0..*
String		 Used to hold the object closure of an association Association
subject_category_closure 0..*
OntologyClass		 Used to hold the subject category closure of an association Association
object_category_closure 0..*
OntologyClass		 Used to hold the object category closure of an association Association
subject_namespace 0..1
String		 Used to hold the subject namespace of an association Association
object_namespace 0..1
String		 Used to hold the object namespace of an association Association
subject_label_closure 0..*
String		 Used to hold the subject label closure of an association Association
object_label_closure 0..*
String		 Used to hold the object label closure of an association Association
retrieval_source_ids 0..*
RetrievalSource		 A list of retrieval sources that served as a source of knowledge expressed in... Association
id 1..1
String		 A unique identifier for an entity Entity
iri 0..1
IriType		 An IRI for an entity Entity
category 0..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String		 rdf:type of biolink:Association should be fixed at rdf:Statement Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity
description 0..1
NarrativeText		 a human-readable description of an entity Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute Entity

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:VariantToGeneAssociation
native biolink:VariantToGeneAssociation

LinkML Source

Direct

name: variant to gene association
description: An association between a variant and a gene, where the variant has a
  genetic association with the gene (i.e. is in linkage disequilibrium)
from_schema: https://w3id.org/biolink/biolink-model
is_a: association
mixins:
- variant to entity association mixin
slot_usage:
  object:
    name: object
    domain_of:
    - association
    range: gene
  predicate:
    name: predicate
    domain_of:
    - predicate mapping
    - association
    subproperty_of: genetically associated with
defining_slots:
- subject
- predicate
- object