Programmatic Access to Gene Ontology

This page documents how to query the ontology, annotations, and GO-CAM models using the GO API.

The purpose of the Biolink Model is to provide a high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc), their properties, relationships, and ways in which they can be associated. The GO API implementation and its associated swagger documentation are available at http://api.geneontology.org/.

In the Biolink Model, any GO term is referred to as “function”, hence the following query returns meta data about the GO term {id}:

/bioentity/function/{id}

Example: annotations for the apoptotic process term

http://api.geneontology.org/api/bioentity/function/GO:0006915

Note: pagination can be achieved by using the start & rows parameter. Example :

http://api.geneontology.org/api/bioentity/function/GO:0006915?start=0&rows=2

Access GO-CAM models

The GO API provides routes for retrieving GO-CAM models and for finding models by taxon or publication. Models are returned in the “user-friendly” GO-CAM JSON format — the same LinkML-defined format available as a release download.

Retrieve a single GO-CAM model by its ID:

https://api.geneontology.org/api/gocam-model/{id}

Example: https://api.geneontology.org/api/gocam-model/5323da1800000002

List all GO-CAM models for a given taxon:

https://api.geneontology.org/api/taxon/{taxon}/models

Example: human GO-CAM models

List all GO-CAM models associated with a publication:

https://api.geneontology.org/api/pmid/{id}/models

Example: models citing PMID:17996703

The full set of routes is documented in the GO API Swagger docs.

Note: the older /api/models/... routes are deprecated and will be removed. The three routes above are the ones to use going forward.