Class: AnatomicalEntity
Description: A subcellular location, cell type or gross anatomical part
classDiagram
class AnatomicalEntity
PhysicalEssence <|-- AnatomicalEntity
OrganismalEntity <|-- AnatomicalEntity
AnatomicalEntity <|-- CellularComponent
AnatomicalEntity <|-- Cell
AnatomicalEntity <|-- GrossAnatomicalStructure
AnatomicalEntity <|-- PathologicalAnatomicalStructure
AnatomicalEntity : category
AnatomicalEntity : deprecated
AnatomicalEntity : description
AnatomicalEntity : full_name
AnatomicalEntity : has_attribute
AnatomicalEntity --|> Attribute : has_attribute
AnatomicalEntity : id
AnatomicalEntity : in_taxon
AnatomicalEntity --|> OrganismTaxon : in_taxon
AnatomicalEntity : in_taxon_label
AnatomicalEntity : iri
AnatomicalEntity : name
AnatomicalEntity : provided_by
AnatomicalEntity : synonym
AnatomicalEntity : type
AnatomicalEntity : xref
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon' |
* OrganismTaxon |
ThingWithTaxon | |
| in_taxon_label: The human readable scientific name for the taxon of the entity. |
0..1 LabelType |
ThingWithTaxon | |
| provided_by: 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. |
* String |
NamedThing | |
| xref: 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. |
* Uriorcurie |
NamedThing | |
| full_name: a long-form human readable name for a thing |
0..1 LabelType |
NamedThing | |
| synonym: Alternate human-readable names for a thing |
* LabelType |
NamedThing | |
| id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1 String |
Entity | |
| iri: An IRI for an entity. This is determined by the id using expansion rules. |
0..1 IriType |
Entity | |
| 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. 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} |
1..* Uriorcurie |
Entity | |
| type: None |
* String |
Entity | |
| name: A human-readable name for an attribute or entity. |
0..1 LabelType |
Entity | |
| description: a human-readable description of an entity |
0..1 NarrativeText |
Entity | |
| has_attribute: may often be an organism attribute |
* Attribute |
Entity | |
| deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Usages
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes, ordered with the most preferred first:
LinkML Source
name: anatomical entity
id_prefixes:
- UBERON
- GO
- CL
- UMLS
- MESH
- NCIT
- EMAPA
- ZFA
- FBbt
- WBbt
description: A subcellular location, cell type or gross anatomical part
in_subset:
- model_organism_database
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- UBERON:0001062
- WIKIDATA:Q4936952
- UMLSSG:ANAT
- STY:T017
- FMA:62955
- CARO:0000000
- SIO:001262
- STY:T029
- STY:T030
related_mappings:
- SNOMEDCT:123037004
narrow_mappings:
- ZFA:0100000
- FBbt:10000000
- EMAPA:0
- MA:0000001
- XAO:0000000
- WBbt:0000100
- NCIT:C12219
- GO:0110165
- STY:T031
is_a: organismal entity
mixins:
- physical essence