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ChemicalToPathwayAssociation

An interaction between a chemical entity and a biological process or pathway.

classDiagram ChemicalToEntityAssociationMixin <|-- ChemicalToPathwayAssociation Association <|-- ChemicalToPathwayAssociation ChemicalToPathwayAssociation : aggregator_knowledge_source ChemicalToPathwayAssociation : category ChemicalToPathwayAssociation : description ChemicalToPathwayAssociation : has_attribute ChemicalToPathwayAssociation : has_evidence ChemicalToPathwayAssociation : id ChemicalToPathwayAssociation : iri ChemicalToPathwayAssociation : knowledge_source ChemicalToPathwayAssociation : name ChemicalToPathwayAssociation : negated ChemicalToPathwayAssociation : object ChemicalToPathwayAssociation : original_knowledge_source ChemicalToPathwayAssociation : predicate ChemicalToPathwayAssociation : primary_knowledge_source ChemicalToPathwayAssociation : publications ChemicalToPathwayAssociation : qualifiers ChemicalToPathwayAssociation : source ChemicalToPathwayAssociation : subject ChemicalToPathwayAssociation : timepoint ChemicalToPathwayAssociation : type

Parent Classes

  • Entity
    • Association
      • ChemicalToPathwayAssociation [ chemical to entity association mixin]

Slots

Name Description
aggregator_knowledge_source An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form.
category Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity, etc. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}
description a human-readable description of an entity
has_attribute connects any entity to an attribute
has_evidence connects an association to an instance of supporting evidence
id A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
iri An IRI for an entity. This is determined by the id using expansion rules.
knowledge_source An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property.
name A human-readable name for an attribute or entity.
negated if set to true, then the association is negated i.e. is not true
object the pathway that is affected by the chemical
original_knowledge_source None
predicate A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.
primary_knowledge_source The most upstream source of the knowledge expressed in an Association that an implementer can identify (may or may not be the 'original' source).
publications connects an association to publications supporting the association
qualifiers connects an association to qualifiers that modify or qualify the meaning of that association
source None
subject the chemical entity that is affecting the pathway
timepoint a point in time
type None

Mappings

Mapping Type Mapped Value
self ['biolink:ChemicalToPathwayAssociation']
native ['biolink:ChemicalToPathwayAssociation']
exact ['SIO:001250']