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Class: OntologyClass

a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.

URI: biolink:OntologyClass

classDiagram class OntologyClass click OntologyClass href "../OntologyClass" OntologyClass <|-- Attribute click Attribute href "../Attribute" OntologyClass <|-- TaxonomicRank click TaxonomicRank href "../TaxonomicRank" OntologyClass <|-- Gene click Gene href "../Gene" OntologyClass <|-- Genome click Genome href "../Genome" OntologyClass : id

Inheritance

Slots

Name Cardinality and Range Description Inheritance
id 1
String		 A unique identifier for an entity direct

Mixin Usage

mixed into description
Attribute A property or characteristic of an entity
Gene A region (or regions) that includes all of the sequence elements necessary to...
Genome A genome is the sum of genetic material within a cell or virion

Usages

used by used in type used
Attribute has_attribute_type range OntologyClass

Examples

Value
UBERON:0000955

Comments

  • This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc
  • Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity

See Also

Identifier and Mapping Information

Valid ID Prefixes

Instances of this class should have identifiers with one of the following prefixes:

  • MESH

  • UMLS

  • KEGG.BRITE

Schema Source

  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema

Mappings

Mapping Type Mapped Value
self biolink:OntologyClass
native bican:OntologyClass
exact owl:Class, schema:Class

LinkML Source

Direct

name: ontology class
id_prefixes:
- MESH
- UMLS
- KEGG.BRITE
definition_uri: https://w3id.org/biolink/vocab/OntologyClass
description: a concept or class in an ontology, vocabulary or thesaurus. Note that
  nodes in a biolink compatible KG can be considered both instances of biolink classes,
  and OWL classes in their own right. In general you should not need to use this class
  directly. Instead, use the appropriate biolink class. For example, for the GO concept
  of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
comments:
- This is modeled as a mixin. 'ontology class' should not be the primary type of a
  node in the KG. Instead you should use an informative bioloink category, such as
  AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL),
  etc
- Note that formally this is a metaclass. Instances of this class are instances in
  the graph, but can be the object of 'type' edges. For example, if we had a node
  in the graph representing a specific brain of a specific patient (e.g brain001),
  this could have a category of bl:Sample, and by typed more specifically with an
  ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
examples:
- value: UBERON:0000955
  description: the class 'brain' from the Uberon anatomy ontology
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
see_also:
- https://github.com/biolink/biolink-model/issues/486
exact_mappings:
- owl:Class
- schema:Class
mixin: true
slots:
- id
class_uri: biolink:OntologyClass

Induced

name: ontology class
id_prefixes:
- MESH
- UMLS
- KEGG.BRITE
definition_uri: https://w3id.org/biolink/vocab/OntologyClass
description: a concept or class in an ontology, vocabulary or thesaurus. Note that
  nodes in a biolink compatible KG can be considered both instances of biolink classes,
  and OWL classes in their own right. In general you should not need to use this class
  directly. Instead, use the appropriate biolink class. For example, for the GO concept
  of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
comments:
- This is modeled as a mixin. 'ontology class' should not be the primary type of a
  node in the KG. Instead you should use an informative bioloink category, such as
  AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL),
  etc
- Note that formally this is a metaclass. Instances of this class are instances in
  the graph, but can be the object of 'type' edges. For example, if we had a node
  in the graph representing a specific brain of a specific patient (e.g brain001),
  this could have a category of bl:Sample, and by typed more specifically with an
  ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
examples:
- value: UBERON:0000955
  description: the class 'brain' from the Uberon anatomy ontology
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
see_also:
- https://github.com/biolink/biolink-model/issues/486
exact_mappings:
- owl:Class
- schema:Class
mixin: true
attributes:
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/id
    description: A unique identifier for an entity. Must be either a CURIE shorthand
      for a URI or a complete URI
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    alias: id
    owner: ontology class
    domain_of:
    - ontology class
    - entity
    - attribute
    - named thing
    - taxonomic rank
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    required: true
class_uri: biolink:OntologyClass