Class: AnatomicalEntity

A subcellular location, cell type or gross anatomical part

URI: biolink:AnatomicalEntity

---

---

Identifier prefixes

• UBERON
• GO
• CL
• UMLS
• MESH
• NCIT

Parents

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

Uses Mixins

• mixin: ThingWithTaxon - A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes
• mixin: PhysicalEssence - Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.

Children

• Cell
• CellularComponent - A location in or around a cell
• GrossAnatomicalStructure
• PathologicalAnatomicalStructure - An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level.

Referenced by class

• AnatomicalEntityToAnatomicalEntityAssociation anatomical entity to anatomical entity association➞object _1..1 AnatomicalEntity
• AnatomicalEntityToAnatomicalEntityAssociation anatomical entity to anatomical entity association➞subject _1..1 AnatomicalEntity
• AnatomicalEntityToAnatomicalEntityOntogenicAssociation anatomical entity to anatomical entity ontogenic association➞object _1..1 AnatomicalEntity
• AnatomicalEntityToAnatomicalEntityOntogenicAssociation anatomical entity to anatomical entity ontogenic association➞subject _1..1 AnatomicalEntity
• AnatomicalEntityToAnatomicalEntityPartOfAssociation anatomical entity to anatomical entity part of association➞object _1..1 AnatomicalEntity
• AnatomicalEntityToAnatomicalEntityPartOfAssociation anatomical entity to anatomical entity part of association➞subject _1..1 AnatomicalEntity
• DiseaseOrPhenotypicFeatureToLocationAssociation disease or phenotypic feature to location association➞object _1..1 AnatomicalEntity
• GeneOrGeneProduct expressed in _0..* AnatomicalEntity
• Association expression site _0..1 AnatomicalEntity
• GeneToExpressionSiteAssociation gene to expression site association➞object _1..1 AnatomicalEntity

Attributes

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..1
  • Range: String
• description _0..1
  • Description: a human-readable description of an entity
  • Range: NarrativeText
  • in subsets: (translator_minimal)
• source _0..1
  • 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 _0..1
  • 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
  • in subsets: (translator_minimal,samples)

Inherited from named thing:

• named thing➞category _1..*
  • 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: NamedThing
  • in subsets: (translator_minimal)

Inherited from organismal entity:

• organismal entity➞has attribute _0..*
  • Description: may often be an organism attribute
  • Range: Attribute
  • in subsets: (samples)

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)

Other properties