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](https://w3id.org/biolink/vocab/OntologyClass)
[String](String.md) | A unique identifier for an entity | direct | ## Mixin Usage | mixed into | description | | --- | --- | | [Attribute](Attribute.md) | A property or characteristic of an entity | | [Gene](Gene.md) | A region (or regions) that includes all of the sequence elements necessary to... | | [Genome](Genome.md) | A genome is the sum of genetic material within a cell or virion | ## Usages | used by | used in | type | used | | --- | --- | --- | --- | | [Attribute](Attribute.md) | [has_attribute_type](has_attribute_type.md) | range | [OntologyClass](OntologyClass.md) | ## 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 * [https://github.com/biolink/biolink-model/issues/486](https://github.com/biolink/biolink-model/issues/486) ## 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://w3id.org/brain-bican/bke-taxonomy ## Mappings | Mapping Type | Mapped Value | | --- | --- | | self | biolink:OntologyClass | | native | bican:OntologyClass | | exact | owl:Class, schema:Class | ## LinkML Source ### Direct
### Induced
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
* **OntologyClass**
* [TaxonomicRank](TaxonomicRank.md)
## Class Properties
| Property | Value |
| --- | --- |
| Class URI | [biolink:OntologyClass](https://w3id.org/biolink/vocab/OntologyClass) |
| Mixin | Yes |
## Slots
| Name | Cardinality and Range | Description | Inheritance |
| --- | --- | --- | --- |
| [id](id.md) | 1 [String](String.md) | A unique identifier for an entity | direct | ## Mixin Usage | mixed into | description | | --- | --- | | [Attribute](Attribute.md) | A property or characteristic of an entity | | [Gene](Gene.md) | A region (or regions) that includes all of the sequence elements necessary to... | | [Genome](Genome.md) | A genome is the sum of genetic material within a cell or virion | ## Usages | used by | used in | type | used | | --- | --- | --- | --- | | [Attribute](Attribute.md) | [has_attribute_type](has_attribute_type.md) | range | [OntologyClass](OntologyClass.md) | ## 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 * [https://github.com/biolink/biolink-model/issues/486](https://github.com/biolink/biolink-model/issues/486) ## 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://w3id.org/brain-bican/bke-taxonomy ## 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://w3id.org/brain-bican/bke-taxonomy
see_also:
- https://github.com/biolink/biolink-model/issues/486
exact_mappings:
- owl:Class
- schema:Class
mixin: true
slots:
- id
class_uri: biolink:OntologyClass
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://w3id.org/brain-bican/bke-taxonomy
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://w3id.org/brain-bican/bke-taxonomy
exact_mappings:
- AGRKB:primaryId
- gff3:ID
- gpi:DB_Object_ID
rank: 1000
domain: entity
slot_uri: biolink:id
identifier: true
owner: ontology class
domain_of:
- ontology class
- entity
- CellTypeTaxonomy
- CellTypeSet
- CellTypeTaxon
- ClusterSet
- Cluster
- Abbreviation
- ColorPalette
- DisplayColor
- attribute
- named thing
- taxonomic rank
- organism taxon
- study result
- relative frequency analysis result
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: string
required: true
class_uri: biolink:OntologyClass