biolink-model

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

• is_a: BiologicalEntity

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
• Bacterium - A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile.
• 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

• ExposureEvent has receptor _0..1 OrganismalEntity
• OrganismalEntityAsAModelOfDiseaseAssociation subject _1..1 OrganismalEntity

Attributes

Own

• has attribute _0..*
  • Description: connects any entity to an attribute
  • Range: Attribute
  • in subsets: (samples)

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}
  • Range: CategoryType
  • in subsets: (translator_minimal)
• type _0..*
  • Range: String
• 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:

• synonym _0..*
  • Description: Alternate human-readable names for a thing
  • Range: LabelType
  • in subsets: (translator_minimal)
• xref _0..*
  • Description: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
  • 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
• full name _0..1
  • Description: a long-form human readable name for a thing
  • Range: LabelType
• 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}
  • Range: CategoryType
  • in subsets: (translator_minimal)

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)
• in taxon label _0..1
  • Description: The human readable scientific name for the taxon of the entity.
  • Range: LabelType
  • in subsets: (translator_minimal)

Domain for slot:

• has attribute _0..*
  • Description: connects any entity to an attribute
  • Range: Attribute
  • in subsets: (samples)

Other properties

Exact Mappings:		WIKIDATA:Q7239
		UMLSSG:LIVB
		CARO:0001010
Narrow Mappings:		STY:T008

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