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Class: OrganismalEntity

A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities

URI: biolink:OrganismalEntity

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Parents

Uses Mixins

  • mixin: SubjectOfInvestigation - An entity that has the role of being studied in an investigation, study, or experiment

Children

  • AnatomicalEntity - A subcellular location, cell type or gross anatomical part
  • CellLine
  • CellularOrganism
  • IndividualOrganism - An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576
  • LifeStage - A stage of development or growth of an organism, including post-natal adult stages
  • PopulationOfIndividualOrganisms - A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes.
  • Virus - A virus is a microorganism that replicates itself as a microRNA and infects the host cell.

Referenced by class

Attributes

Own

Inherited from entity:

  • id 1..1
    • 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 0..1
    • 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 0..*
  • description 0..1
    • Description: a human-readable description of an entity
    • Range: NarrativeText
    • in subsets: (translator_minimal)
  • has attribute 0..*
    • Description: connects any entity to an attribute
    • Range: Attribute
    • in subsets: (samples)

Inherited from gene product mixin:

  • xref 0..*
    • Description: Alternate CURIEs for a thing
    • Range: Uriorcurie
    • in subsets: (translator_minimal)

Inherited from macromolecular machine mixin:

  • name 0..1
    • Description: A human-readable name for an attribute or entity.
    • Range: LabelType
    • in subsets: (translator_minimal,samples)

Inherited from named thing:

  • provided by 0..*
    • Description: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
    • Range: String
  • 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}

Inherited from thing with taxon:

  • in taxon 0..*
    • Description: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see ‘thing with taxon’
    • Range: OrganismTaxon
    • in subsets: (translator_minimal)

Domain for slot:

Other properties

     
Exact Mappings:   WIKIDATA:Q7239
    UMLSSG:LIVB
    CARO:0001010