Link

Class: PhysiologicalProcess

URI: biolink:PhysiologicalProcess


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Identifier prefixes

  • GO
  • REACT

Parents

  • is_a: BiologicalProcess - One or more causally connected executions of molecular functions

Uses Mixins

  • mixin: OntologyClass - a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.

Attributes

Inherited from biological process or activity:

  • enabled by 0..*
    • Description: holds between a process and a physical entity, where the physical entity executes the process
    • range: PhysicalEntity
    • in subsets: (translator_minimal)

Inherited from entity:

  • id REQ
    • Description: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
    • range: String
    • in subsets: (translator_minimal)
  • iri OPT
    • Description: An IRI for an entity. This is determined by the id using expansion rules.
    • range: IriType
    • in subsets: (translator_minimal,samples)
  • category 0..*
    • Description: 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, … 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}
  • type OPT
  • description OPT
    • Description: a human-readable description of an entity
    • range: NarrativeText
    • in subsets: (translator_minimal)
  • source OPT
    • Description: a lightweight analog to the association class ‘has provider’ slot, which is the string name, or the authoritative (i.e. database) namespace, designating the origin of the entity to which the slot belongs.
    • range: LabelType
    • in subsets: (translator_minimal)
  • provided by 0..*
    • Description: connects an association to the agent (person, organization or group) that provided it
    • range: Agent
  • has attribute 0..*
    • Description: connects any entity to an attribute
    • range: Attribute
    • in subsets: (samples)

Inherited from macromolecular machine mixin:

  • macromolecular machine mixin➞name OPT
    • Description: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
    • range: SymbolType

Inherited from named thing:

Other properties

     
Aliases:   physiology
Exact Mappings:   UMLSSC:T039
    UMLSST:phsf
    WIKIDATA:Q30892994
Narrow Mappings:   UMLSSC:T040
    UMLSST:orgf
    UMLSSC:T042
    UMLSST:ortf
    UMLSSC:T043
    UMLSST:celf
    UMLSSC:T045
    UMLSST:genf