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Class: BiologicalEntity (Abstract)

Aliases: bioentity

classDiagram class BiologicalEntity ThingWithTaxon <|-- BiologicalEntity NamedThing <|-- BiologicalEntity BiologicalEntity <|-- RegulatoryRegion BiologicalEntity <|-- BiologicalProcessOrActivity BiologicalEntity <|-- GeneticInheritance BiologicalEntity <|-- OrganismalEntity BiologicalEntity <|-- DiseaseOrPhenotypicFeature BiologicalEntity <|-- Gene BiologicalEntity <|-- MacromolecularComplex BiologicalEntity <|-- NucleosomeModification BiologicalEntity <|-- Genome BiologicalEntity <|-- Exon BiologicalEntity <|-- Transcript BiologicalEntity <|-- CodingSequence BiologicalEntity <|-- Polypeptide BiologicalEntity <|-- ProteinDomain BiologicalEntity <|-- PosttranslationalModification BiologicalEntity <|-- ProteinFamily BiologicalEntity <|-- NucleicAcidSequenceMotif BiologicalEntity <|-- GeneFamily BiologicalEntity <|-- Genotype BiologicalEntity <|-- Haplotype BiologicalEntity <|-- SequenceVariant BiologicalEntity <|-- ReagentTargetedGene BiologicalEntity : category BiologicalEntity : deprecated BiologicalEntity : description BiologicalEntity : full_name BiologicalEntity : has_attribute BiologicalEntity --|> Attribute : has_attribute BiologicalEntity : id BiologicalEntity : in_taxon BiologicalEntity --|> OrganismTaxon : in_taxon BiologicalEntity : in_taxon_label BiologicalEntity : iri BiologicalEntity : name BiologicalEntity : provided_by BiologicalEntity : synonym BiologicalEntity : type BiologicalEntity : 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:
connects any entity to an attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

LinkML Source

name: biological entity
from_schema: https://w3id.org/biolink/biolink-model
aliases:
- bioentity
narrow_mappings:
- WIKIDATA:Q28845870
- STY:T050
- SIO:010046
- STY:T129
is_a: named thing
abstract: true
mixins:
- thing with taxon