Taxonomy-based partitioning of the Gene Ontology

The Gene Ontology (GO) project is a collaborative effort to construct ontologies which facilitate biologically meaningful annotation of gene products. In some situations, only a generic or a species-specific subset of all GO terms is required to annotate and analyze the results of a particular biomedical experiment. We show that by defining explicit links between terms in the GO and terms in the Taxonomy of Species (TS) it is possible to automatically create partitions of the GO according to various taxonomic criteria.Our framework is based on three logically defined relations—validity, specificity, and relevance—used to link terms in the Gene Ontology with terms in the Taxonomy. The major advantages of this approach, as compared to the traditional GO slims methodology, are: unambiguous semantics of GO–TS annotations, significant reduction of the effort needed to manually select GO terms appropriate for a particular taxonomic context, ability to generate views of the GO even for taxa for which no explicit links with GO terms exist, logical consistency of such views, and automated updates of TS-dependent GO subsets. Incorporation of the proposed framework into the GO may improve the usability of the ontology for those scientists who focus their research on a particular species or a specific class of organisms.