GOcats: A tool for categorizing Gene Ontology into subgraphs of user-defined concepts

Gene Ontology is used extensively in scientific knowledgebases and repositories to organize the wealth of available biological information. However, interpreting annotations derived from differential gene lists is difficult without manually sorting into higher-order categories. To address these issues, we present GOcats, a novel tool that organizes the Gene Ontology (GO) into subgraphs representing user-defined concepts, while ensuring that all appropriate relations are congruent with respect to scoping semantics. We tested GOcats performance using subcellular location categories to mine annotations from GO-utilizing knowledgebases and evaluating their accuracy against immunohistochemistry datasets in the Human Protein Atlas (HPA). In comparison to mappings generated from UniProt’s controlled vocabulary and from GO slims via OWLTools’ Map2Slim, GOcats outperforms these methods without reliance on a human-curated set of GO terms. By identifying and properly defining relations with respect to semantic scope, GOcats can use traditionally problematic relations without encountering erroneous term mapping. We applied GOcats in the comparison of HPA-sourced knowledgebase annotations to experimentally-derived annotations provided by HPA directly. During the comparison, GOcats improved correspondence between the annotation sources by adjusting semantic granularity. Utilized in this way, GOcats can perform an accurate knowledgebase-level evaluation of curated HPA-based annotations.