STOP Using Just GO: A Multi-Ontology Enrichment Analysis Tool
Enrichment analysis is a common technique used by biologists to reduce a large set of annotations to a smaller, more manageable set of significantly represented concepts. Currently, enrichment analysis is done primarily using Gene Ontology (GO). Although GO has been useful, there are entire domains of research that are not considered as part of that ontology (such as diseases or phenotypes). To solve this problem, we have created Statistical Tracking of Ontological Phrases (STOP), a multi-ontology enrichment analysis tool. STOP gathers text related to genes from the public databases and automatically annotates it using the Stanford NCBO Annotator. STOP performs enrichment analysis on all of the ontologies annotated. Users can select their own background dataset, or use a predefined background of the entire genome, or proteome for a given species. This project shows that multiple ontologies provide more useful information than single ontologies.