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Class: GeneToGeneAssociation

abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.

  • NOTE: this is an abstract class and should not be instantiated directly

URI: biolink:GeneToGeneAssociation

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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subject 1..1
GeneOrGeneProduct
the subject gene in the association Association
predicate 1..1
PredicateType
A high-level grouping for the relationship type Association
object 1..1
GeneOrGeneProduct
the object gene in 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

Aliases

  • molecular or genetic interaction

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: gene to gene association
description: abstract parent class for different kinds of gene-gene or gene product
  to gene product relationships. Includes homology and interaction.
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- molecular or genetic interaction
is_a: association
abstract: true
slot_usage:
  subject:
    name: subject
    description: the subject gene in the association. If the relation is symmetric,
      subject vs object is arbitrary. We allow a gene product to stand as a proxy
      for the gene or vice versa.
    domain_of:
    - association
    range: gene or gene product
  object:
    name: object
    description: the object gene in the association. If the relation is symmetric,
      subject vs object is arbitrary. We allow a gene product to stand as a proxy
      for the gene or vice versa.
    domain_of:
    - association
    range: gene or gene product
defining_slots:
- subject
- object