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.
- GeneOntologyClass - an ontology class that describes a functional aspect of a gene, gene prodoct or complex
- RelationshipType - An OWL property used as an edge label
- TaxonomicRank - A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)
- UnclassifiedOntologyClass - this is used for nodes that are taken from an ontology but are not typed using an existing biolink class
- Attribute (mixin) - A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.
- Behavior (mixin)
- BiologicalProcess (mixin) - One or more causally connected executions of molecular functions
- BiologicalProcessOrActivity (mixin) - Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system.
- Drug (mixin) - A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease
- MolecularActivity (mixin) - An execution of a molecular function carried out by a gene product or macromolecular complex.
- Pathway (mixin)
- PhysiologicalProcess (mixin)
- ClinicalMeasurement clinical measurement➞has attribute type REQ OntologyClass
- ContributorAssociation contributor association➞qualifiers 0..* OntologyClass
- GeneExpressionMixin gene expression mixin➞quantifier qualifier OPT OntologyClass
- GeneToExpressionSiteAssociation gene to expression site association➞quantifier qualifier OPT OntologyClass
- Attribute has attribute type REQ OntologyClass
- NamedThing has molecular consequence 0..* OntologyClass
- NamedThing has topic OPT OntologyClass
- Association interacting molecules category OPT OntologyClass
- Association qualifiers 0..* OntologyClass
- Association quantifier qualifier OPT OntologyClass
- OntologyClass subclass of 0..* OntologyClass
- OntologyClass superclass of 0..* OntologyClass
|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:||Example(value=’UBERON:0000955’, description=”the class ‘brain’ from the Uberon anatomy ontology”)|