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Class: GeneAffectsChemicalAssociation

Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)

URI: biolink:GeneAffectsChemicalAssociation

classDiagram class GeneAffectsChemicalAssociation Association <|-- GeneAffectsChemicalAssociation GeneAffectsChemicalAssociation : aggregator_knowledge_source GeneAffectsChemicalAssociation : anatomical_context_qualifier GeneAffectsChemicalAssociation --|> anatomical entity : anatomical_context_qualifier GeneAffectsChemicalAssociation : category GeneAffectsChemicalAssociation : causal_mechanism_qualifier GeneAffectsChemicalAssociation --|> CausalMechanismQualifierEnum : causal_mechanism_qualifier GeneAffectsChemicalAssociation : description GeneAffectsChemicalAssociation : has_attribute GeneAffectsChemicalAssociation --|> attribute : has_attribute GeneAffectsChemicalAssociation : has_evidence GeneAffectsChemicalAssociation --|> evidence type : has_evidence GeneAffectsChemicalAssociation : id GeneAffectsChemicalAssociation : iri GeneAffectsChemicalAssociation : knowledge_source GeneAffectsChemicalAssociation : name GeneAffectsChemicalAssociation : negated GeneAffectsChemicalAssociation : object GeneAffectsChemicalAssociation --|> chemical entity : object GeneAffectsChemicalAssociation : object_aspect_qualifier GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : object_aspect_qualifier GeneAffectsChemicalAssociation : object_category GeneAffectsChemicalAssociation --|> ontology class : object_category GeneAffectsChemicalAssociation : object_category_closure GeneAffectsChemicalAssociation --|> ontology class : object_category_closure GeneAffectsChemicalAssociation : object_closure GeneAffectsChemicalAssociation : object_context_qualifier GeneAffectsChemicalAssociation --|> anatomical entity : object_context_qualifier GeneAffectsChemicalAssociation : object_form_or_variant_qualifier GeneAffectsChemicalAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : object_form_or_variant_qualifier GeneAffectsChemicalAssociation : object_label_closure GeneAffectsChemicalAssociation : object_namespace GeneAffectsChemicalAssociation : object_part_qualifier GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalPartQualifierEnum : object_part_qualifier GeneAffectsChemicalAssociation : original_object GeneAffectsChemicalAssociation : original_predicate GeneAffectsChemicalAssociation : original_subject GeneAffectsChemicalAssociation : predicate GeneAffectsChemicalAssociation : primary_knowledge_source GeneAffectsChemicalAssociation : publications GeneAffectsChemicalAssociation --|> publication : publications GeneAffectsChemicalAssociation : qualified_predicate GeneAffectsChemicalAssociation : qualifiers GeneAffectsChemicalAssociation --|> ontology class : qualifiers GeneAffectsChemicalAssociation : retrieval_source_ids GeneAffectsChemicalAssociation --|> retrieval source : retrieval_source_ids GeneAffectsChemicalAssociation : subject GeneAffectsChemicalAssociation --|> gene or gene product : subject GeneAffectsChemicalAssociation : subject_aspect_qualifier GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier GeneAffectsChemicalAssociation : subject_category GeneAffectsChemicalAssociation --|> ontology class : subject_category GeneAffectsChemicalAssociation : subject_category_closure GeneAffectsChemicalAssociation --|> ontology class : subject_category_closure GeneAffectsChemicalAssociation : subject_closure GeneAffectsChemicalAssociation : subject_context_qualifier GeneAffectsChemicalAssociation --|> anatomical entity : subject_context_qualifier GeneAffectsChemicalAssociation : subject_derivative_qualifier GeneAffectsChemicalAssociation : subject_direction_qualifier GeneAffectsChemicalAssociation --|> DirectionQualifierEnum : subject_direction_qualifier GeneAffectsChemicalAssociation : subject_form_or_variant_qualifier GeneAffectsChemicalAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : subject_form_or_variant_qualifier GeneAffectsChemicalAssociation : subject_label_closure GeneAffectsChemicalAssociation : subject_namespace GeneAffectsChemicalAssociation : subject_part_qualifier GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalPartQualifierEnum : subject_part_qualifier GeneAffectsChemicalAssociation : timepoint GeneAffectsChemicalAssociation : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subject_form_or_variant_qualifier 0..1
ChemicalOrGeneOrGeneProductFormOrVariantEnum		 direct
subject_part_qualifier 0..1
GeneOrGeneProductOrChemicalPartQualifierEnum		 direct
subject_derivative_qualifier 0..1
String		 direct
subject_aspect_qualifier 0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 direct
subject_context_qualifier 0..1
AnatomicalEntity		 direct
subject_direction_qualifier 0..1
DirectionQualifierEnum		 direct
object_form_or_variant_qualifier 0..1
ChemicalOrGeneOrGeneProductFormOrVariantEnum		 direct
object_part_qualifier 0..1
GeneOrGeneProductOrChemicalPartQualifierEnum		 direct
object_aspect_qualifier 0..1
GeneOrGeneProductOrChemicalEntityAspectEnum		 direct
object_context_qualifier 0..1
AnatomicalEntity		 direct
causal_mechanism_qualifier 0..1
CausalMechanismQualifierEnum		 A statement qualifier representing a type of molecular control mechanism thro... direct
anatomical_context_qualifier 0..1
AnatomicalEntity		 A statement qualifier representing an anatomical location where an relationsh... direct
qualified_predicate 0..1
String		 Predicate to be used in an association when subject and object qualifiers are... direct
subject 1..1
GeneOrGeneProduct		 connects an association to the subject of the association Association
predicate 1..1
PredicateType		 A high-level grouping for the relationship type Association
object 1..1
ChemicalEntity		 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

Examples

Value
JsonObj(subject='TRPC4', predicate='affects', object='Barium', object_aspect_qualifier='transport', object_direction_qualifier='increased')

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: gene affects chemical association
description: Describes an effect that a gene or gene product has on a chemical entity
  (e.g. an impact of on its abundance, activity,localization, processing, expression,
  etc.)
examples:
- value: JsonObj(subject='TRPC4', predicate='affects', object='Barium', object_aspect_qualifier='transport',
    object_direction_qualifier='increased')
from_schema: https://w3id.org/biolink/biolink-model
is_a: association
slots:
- subject form or variant qualifier
- subject part qualifier
- subject derivative qualifier
- subject aspect qualifier
- subject context qualifier
- subject direction qualifier
- object form or variant qualifier
- object part qualifier
- object aspect qualifier
- object context qualifier
- causal mechanism qualifier
- anatomical context qualifier
- qualified predicate
slot_usage:
  subject:
    name: subject
    domain_of:
    - association
    range: gene or gene product
  subject form or variant qualifier:
    name: subject form or variant qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    - gene has variant that contributes to disease association
    range: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  subject part qualifier:
    name: subject part qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    range: GeneOrGeneProductOrChemicalPartQualifierEnum
  subject aspect qualifier:
    name: subject aspect qualifier
    domain_of:
    - predicate mapping
    - chemical affects gene association
    - gene affects chemical association
    - gene to disease or phenotypic feature association
    range: GeneOrGeneProductOrChemicalEntityAspectEnum
  subject context qualifier:
    name: subject context qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    range: anatomical entity
  subject direction qualifier:
    name: subject direction qualifier
    domain_of:
    - predicate mapping
    - chemical affects gene association
    - gene affects chemical association
    range: DirectionQualifierEnum
  predicate:
    name: predicate
    domain_of:
    - predicate mapping
    - association
    subproperty_of: affects
  qualified predicate:
    name: qualified predicate
    domain_of:
    - predicate mapping
    - chemical affects gene association
    - gene affects chemical association
    subproperty_of: causes
  object:
    name: object
    domain_of:
    - association
    range: chemical entity
  object form or variant qualifier:
    name: object form or variant qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    range: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  object part qualifier:
    name: object part qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    range: GeneOrGeneProductOrChemicalPartQualifierEnum
  object derivative qualifier:
    name: object derivative qualifier
    range: ChemicalEntityDerivativeEnum
  object aspect qualifier:
    name: object aspect qualifier
    domain_of:
    - predicate mapping
    - chemical affects gene association
    - gene affects chemical association
    range: GeneOrGeneProductOrChemicalEntityAspectEnum
  object context qualifier:
    name: object context qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    range: anatomical entity
  object direction qualifier:
    name: object direction qualifier
    range: DirectionQualifierEnum
  causal mechanism qualifier:
    name: causal mechanism qualifier
    domain_of:
    - predicate mapping
    - chemical affects gene association
    - gene affects chemical association
    range: CausalMechanismQualifierEnum
  anatomical context qualifier:
    name: anatomical context qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    range: anatomical entity
  species context qualifier:
    name: species context qualifier
    range: organism taxon