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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 : equivalent_identifiers BiologicalEntity : full_name BiologicalEntity : has_attribute BiologicalEntity --|> Attribute : has_attribute BiologicalEntity : id BiologicalEntity : in_taxon BiologicalEntity --|> OrganismTaxon : in_taxon BiologicalEntity : in_taxon_label BiologicalEntity : information_content 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
information_content:
Information content (IC) value for a term, primarily from Automats. 		0..1
Float		 NamedThing
equivalent_identifiers:
A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is used to represent a collection of identifiers that are considered equivalent to the primary identifier of an entity. These equivalent identifiers may come from different databases, ontologies, or naming conventions, but they all refer to the same underlying concept or entity. This attribute is particularly useful in data integration and interoperability scenarios, where it is important to recognize and link different representations of the same entity across various sources. 		*
Uriorcurie		 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

Usages

used by used in type used
ChemicalAffectsBiologicalEntityAssociation object range BiologicalEntity
ChemicalAffectsGeneAssociation object range BiologicalEntity

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