Using OWL to model biological knowledge

TLDR: The disciplines of biology and bioinformatics are used to reveal the requirements of a community that both needs and uses ontologies, and what OWL-DL and its underlying description logic either cannot handle in theory or because of lack of implementation.

Abstract: Much has been written of the facilities for ontology building and reasoning offered for ontologies expressed in the Web Ontology Language (OWL). Less has been written about how the modelling requirements of different areas of interest are met by OWL-DL's underlying model of the world. In this paper we use the disciplines of biology and bioinformatics to reveal the requirements of a community that both needs and uses ontologies. We use a case study of building an ontology of protein phosphatases to show how OWL-DL's model can capture a large proportion of the community's needs. We demonstrate how Ontology Design Patterns (ODPs) can extend inherent limitations of this model. We give examples of relationships between more than two instances; lists and exceptions, and conclude by illustrating what OWL-DL and its underlying description logic either cannot handle in theory or because of lack of implementation. Finally, we present a research agenda that, if fulfilled, would help ensure OWL's wider take up in the life science community.