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.