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Class: GeneToPathwayAssociation

An interaction between a gene or gene product and a biological process or pathway.

URI: biolink:GeneToPathwayAssociation

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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subject 1..1
GeneOrGeneProduct		 the gene or gene product entity that participates or influences the pathway Association
predicate 1..1
PredicateType		 A high-level grouping for the relationship type Association
object 1..1
Pathway		 the pathway that includes or is affected by the gene or gene product 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:GeneToPathwayAssociation
native biolink:GeneToPathwayAssociation

LinkML Source

Direct

name: gene to pathway association
description: An interaction between a gene or gene product and a biological process
  or pathway.
from_schema: https://w3id.org/biolink/biolink-model
is_a: association
mixins:
- gene to entity association mixin
slot_usage:
  subject:
    name: subject
    description: the gene or gene product entity that participates or influences the
      pathway
    domain_of:
    - association
    range: gene or gene product
  object:
    name: object
    description: the pathway that includes or is affected by the gene or gene product
    domain_of:
    - association
    range: pathway
defining_slots:
- subject
- object