Ontologies in Bioinformatics

Molecular biology offers a large, complex and volatile domain that tests knowledge representation techniques to the limit of their fidelity, precision, expressivity and adaptability. The discipline of molecular biology and bioinformatics relies greatly on the use of community knowledge, rather than laws and axioms, to further understanding, and knowledge generation. This knowledge has traditionally been kept as natural language. Given the exponential growth of already large quantities of data and associated knowledge, this is an unsustainable form of representation. This knowledge needs to be stored in a computationally amenable form and ontologies offer a mechanism for creating a shared understanding of a community for both humans and computers. Ontologies have been built and used for many domains and this chapter explores their role within bioinformatics. Structured classifications have a long history in biology; not least in the Linnean description of species. The explicit use of ontologies, however, is more recent. This chapter provides a survey of the need for ontologies; the nature of the domain and the knowledge tasks involved; and then an overview of ontology work in the discipline. The widest use of ontologies within biology is for conceptual annotation — a representation of stored knowledge more computationally amenable than natural language. An ontology also offers a means to create the illusion of a common query interface over diverse, distributed information sources — here an ontology creates a shared understanding for the user and also a means to computationally reconcile heterogeneities between the resources. Ontologies also provide a means for a schema definition suitable for the complexity and precision required for biology’s knowledge bases. Coming right up to date, bioinformatics is well set as an exemplar of the Semantic Web, offering both web accessible content and services conceptually marked up as a means for computational exploitation of its resources — this theme is explored through the myGRID services ontology. Ontologies in bioinformatics cover a wide range of usages and representation styles. Bioinformatics offers an exciting application area in which the community can see a real need for ontology based technology to work and deliver its promise.