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A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations.
One of the main uses of the model is as a way of standardizing types and relational structures in knowledge graphs (KGs), where the KG may be either a property graph or RDF.
The schema is expressed as a yaml file, which is translated into:
- Individual pages for each class in the model, e.g https://w3id.org/biolink/vocab/Gene
- An OWL ontology, also available on bioportal
- ShEx (RDF shape constraints)
- (Experimental) graphql, protobuf, json-schema
The schema assumes a property graph, where nodes represent individual entities, and edges represent associations between nodes. The biolink model provides a schema for both nodes and edges.
- named thing - all nodes are a sub class of 'named thing'
- association - all edges are a sub class of 'association'
- Slots - slots are used to collectively refer to, both, node and edge properties.
- node property - all node properties are a sub class of 'node property'
- association slot - all edge properties are a sub class of 'association slot'
See the Datamodel index for a list nodes, edges, and slots.
See biolink json-ld context to see CURIE prefix mappings.
The includes prefix expansions such as:
"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
"NCBIGene": "http://www.ncbi.nlm.nih.gov/gene/",
"NCIT": "http://purl.obolibrary.org/obo/NCIT_",
Following the JSON-LD context standard.
Note that we do not curate these in biolink. Rather we take these from upstream sources, via prefixcommons biocontexts. We specify a priority order of upstream sources in cases where conflicts may occur. See the default_curi_maps tag at the top of the biolink-model.yaml file. We also specify a small set of top-level overrides via the prefixes tag at the top.
See mapping to neo4j
See mapping to RDF