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Class: ChemicalGeneInteractionAssociation

describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)

URI: biolink:ChemicalGeneInteractionAssociation

classDiagram class ChemicalGeneInteractionAssociation ChemicalToEntityAssociationMixin <|-- ChemicalGeneInteractionAssociation Association <|-- ChemicalGeneInteractionAssociation ChemicalGeneInteractionAssociation : aggregator_knowledge_source ChemicalGeneInteractionAssociation : anatomical_context_qualifier ChemicalGeneInteractionAssociation --|> anatomical entity : anatomical_context_qualifier ChemicalGeneInteractionAssociation : category ChemicalGeneInteractionAssociation : description ChemicalGeneInteractionAssociation : has_attribute ChemicalGeneInteractionAssociation --|> attribute : has_attribute ChemicalGeneInteractionAssociation : has_evidence ChemicalGeneInteractionAssociation --|> evidence type : has_evidence ChemicalGeneInteractionAssociation : id ChemicalGeneInteractionAssociation : iri ChemicalGeneInteractionAssociation : knowledge_source ChemicalGeneInteractionAssociation : name ChemicalGeneInteractionAssociation : negated ChemicalGeneInteractionAssociation : object ChemicalGeneInteractionAssociation --|> gene or gene product : object ChemicalGeneInteractionAssociation : object_category ChemicalGeneInteractionAssociation --|> ontology class : object_category ChemicalGeneInteractionAssociation : object_category_closure ChemicalGeneInteractionAssociation --|> ontology class : object_category_closure ChemicalGeneInteractionAssociation : object_closure ChemicalGeneInteractionAssociation : object_context_qualifier ChemicalGeneInteractionAssociation --|> anatomical entity : object_context_qualifier ChemicalGeneInteractionAssociation : object_form_or_variant_qualifier ChemicalGeneInteractionAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : object_form_or_variant_qualifier ChemicalGeneInteractionAssociation : object_label_closure ChemicalGeneInteractionAssociation : object_namespace ChemicalGeneInteractionAssociation : object_part_qualifier ChemicalGeneInteractionAssociation --|> GeneOrGeneProductOrChemicalPartQualifierEnum : object_part_qualifier ChemicalGeneInteractionAssociation : original_object ChemicalGeneInteractionAssociation : original_predicate ChemicalGeneInteractionAssociation : original_subject ChemicalGeneInteractionAssociation : predicate ChemicalGeneInteractionAssociation : primary_knowledge_source ChemicalGeneInteractionAssociation : publications ChemicalGeneInteractionAssociation --|> publication : publications ChemicalGeneInteractionAssociation : qualifiers ChemicalGeneInteractionAssociation --|> ontology class : qualifiers ChemicalGeneInteractionAssociation : retrieval_source_ids ChemicalGeneInteractionAssociation --|> retrieval source : retrieval_source_ids ChemicalGeneInteractionAssociation : subject ChemicalGeneInteractionAssociation --|> chemical entity : subject ChemicalGeneInteractionAssociation : subject_category ChemicalGeneInteractionAssociation --|> ontology class : subject_category ChemicalGeneInteractionAssociation : subject_category_closure ChemicalGeneInteractionAssociation --|> ontology class : subject_category_closure ChemicalGeneInteractionAssociation : subject_closure ChemicalGeneInteractionAssociation : subject_context_qualifier ChemicalGeneInteractionAssociation --|> anatomical entity : subject_context_qualifier ChemicalGeneInteractionAssociation : subject_derivative_qualifier ChemicalGeneInteractionAssociation --|> ChemicalEntityDerivativeEnum : subject_derivative_qualifier ChemicalGeneInteractionAssociation : subject_form_or_variant_qualifier ChemicalGeneInteractionAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : subject_form_or_variant_qualifier ChemicalGeneInteractionAssociation : subject_label_closure ChemicalGeneInteractionAssociation : subject_namespace ChemicalGeneInteractionAssociation : subject_part_qualifier ChemicalGeneInteractionAssociation --|> GeneOrGeneProductOrChemicalPartQualifierEnum : subject_part_qualifier ChemicalGeneInteractionAssociation : timepoint ChemicalGeneInteractionAssociation : 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
ChemicalEntityDerivativeEnum		 direct
subject_context_qualifier 0..1
AnatomicalEntity		 direct
object_form_or_variant_qualifier 0..1
ChemicalOrGeneOrGeneProductFormOrVariantEnum		 direct
object_part_qualifier 0..1
GeneOrGeneProductOrChemicalPartQualifierEnum		 direct
object_context_qualifier 0..1
AnatomicalEntity		 direct
anatomical_context_qualifier 0..1
AnatomicalEntity		 A statement qualifier representing an anatomical location where an relationsh... direct
subject 1..1
ChemicalEntity		 the chemical entity or entity that is an interactor Association
predicate 1..1
PredicateType		 A high-level grouping for the relationship type Association
object 1..1
GeneOrGeneProduct		 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:ChemicalGeneInteractionAssociation
native biolink:ChemicalGeneInteractionAssociation
exact SIO:001257

LinkML Source

Direct

name: chemical gene interaction association
description: describes a physical interaction between a chemical entity and a gene
  or gene product. Any biological or chemical effect resulting from such an interaction
  are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact
  of a chemical on the abundance, activity, structure, etc, of either participant
  in the interaction)
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- SIO:001257
is_a: association
mixins:
- chemical to entity association mixin
slots:
- subject form or variant qualifier
- subject part qualifier
- subject derivative qualifier
- subject context qualifier
- object form or variant qualifier
- object part qualifier
- object context qualifier
- anatomical context qualifier
slot_usage:
  subject:
    name: subject
    domain_of:
    - association
    range: chemical entity
  object:
    name: object
    domain_of:
    - association
    range: gene or gene product
  predicate:
    name: predicate
    domain_of:
    - predicate mapping
    - association
    subproperty_of: physically interacts with
  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 derivative qualifier:
    name: subject derivative qualifier
    domain_of:
    - predicate mapping
    - chemical gene interaction association
    - chemical affects gene association
    - gene affects chemical association
    range: ChemicalEntityDerivativeEnum
  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
  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 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
  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