The relative simplicity of standard GO annotations enabled their widespread use by allowing users to ask actionable biological questions (e.g. ‘what are the functions of a given gene’; ‘what are the scientific articles and the experimental evidence supporting that a gene has a certain function’). The rich semantic structure of GO-CAMs provided by OWL increases both the expressivity of the information captured by curators and gives the ability to perform more complex and targeted queries. The GO-CAM formalism thus enables queries such as ‘which genes’ activities are upstream or downstream of a given activity or process’ or ‘which genes’ activities directly positively regulate a given activity’. These advanced queries are designed with the SPARQL Query Language (https://www.w3.org/TR/sparql11-overview/) using the GO SPARQL endpoint http://sparql.geneontology.org. In addition, SPARQL enables the interoperability of RDF/OWL databases through federated queries (https://www.w3.org/TR/sparql11-federated-query/) (22). Federated queries allow, for instance, to query features of a GO-CAM and enrich these features with additional information available at other SPARQL endpoints such as UniProt (https://sparql.uniprot.org), identifiers.org (https://ebi.identifiers.org/services/sparql) and wikipathway (http://sparql.wikipathways.org).
