The Biolink Model is a high level datamodel of biological entities (genes, diseases, phenotypes, pathways,
individuals, substances, etc) and their associations.
The model itself is designed as a way of standardizing types and relational structures in knowledge graphs (KGs),
where the KG may be either a property graph or RDF triple store.
Biolink Model is authored and developed with the BiolinkML framework.
The schema is expressed as a YAML, which is translated to,
- Individual pages for each class in the model, e.g biolink:Gene
- An OWL ontology, also available on BioPortal
- Python dataclasses, also available on PyPI
- ShEx (RDF shape constraints)
- graphql (Experimental)
- protobuf (Experimental)
- json-schema (Experimental)
The schema assumes a property graph, where nodes represent individual entities, and edges represent associations
between entities. Biolink Model provides a schema for representing both nodes and edges.
The model itself can be divided into three parts,
- Entities (Nodes)
- Associations (Edges)
- Slots (Properties)
The Biolink Model serves as the core datamodel for the Biolink API, an API for accessing biological knowledge.