Programmatic Access to Gene Ontology

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This page documents various ways to query the ontology and annotations using the GO APIs

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Query GO ontology and annotations with Biolink

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

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Query GO Causal Activity Models (SPARQL endpoint)

GO provides an experimental SPARQL endpoint to query both the GO ontology and GO-CAMs. Please refer to the RDF/SPARQL documentation to learn about the how GO-CAMs are represented in RDF and queries through SPARQL.

Already a GO-CAM/SPARQL expert ? [ Access GO SPARQL endpoint ]