Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)

Motivation: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protege-2000, to the maintenance and development of GO. Results: We transferred GO to Protege-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protege Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protege-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts. Availability: Gene Ontology in Protege-2000 and the associated code are located at http://smi.stanford.edu/ projects/helix/gokbms/. Protege-2000 is available from http://protege.stanford.edu. Contact: russ.altman@stanford.edu.