TABLE 1.
Biolink Model elements and their definitions
| Biolink Model element | Definition | Examples |
|---|---|---|
| Class | High‐level types (or categories) representing core biological concepts of interest such as genes, diseases, chemical substances, anatomic structures, and phenotypic features, arranged in a class hierarchy | biolink:Disease, biolink:PhenotypicFeature, biolink:Gene, biolink:SequenceVariant |
| Predicate | Objects that define the action being carried out by the subject (or named entity) of a core triple and help define how two entities (or classes) can be related to one another. In graph formalism, predicates are relationships that link two instances. Predicates in the Biolink Model all descend from the “biolink:related_to” predicate | biolink:has_phenotype, biolink:positively_regulates, biolink:affects, biolink:associated_with, biolink:related_to |
| Node property | A set of attributes that can be regarded as a characteristic or inherent part of an instance of “biolink:NamedThing” | biolink:symbol, biolink:name, biolink:id |
| Edge property | A set of attributes that can be regarded as a characteristic or inherent part of a statement, association, or edge | biolink:publications, biolink:has_evidence |
| Core triple | The domain knowledge of an association expressed by the subject and object nodes plus the predicate connecting them | biolink:Disease biolink:has_phenotype biolink:PhenotypicFeature |
| Association | Associations are classes that define a relationship between two domain concepts, constrained and qualified by edge attributes | biolink:DiseaseToPhenotypicFeatureAssociation, biolink:GeneToDiseaseAssociation |
| Type | A kind of value that tells what operations can be performed on a particular data set. Biolink Model implements common types, such as integer and string, but it also defines custom types like quotient and unit | URI or CURIE, string, integer, biolink:Quotient, biolink:Unit |
| Mixin | Modeling elements used to extend the properties (or slots) of a class, without changing its position in the class hierarchy. Please see the Biolink Model documentation for more information on mixin elements | biolink:GeneOrGeneProduct, biolink:DiseaseOrPhenotypicFeature |
Abbreviations: CURIE, compact URI; URI, unique resource identifier.