The Logic of Biological Classification and the Foundations of Biomedical Ontology

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. Introduction In reflection of the huge amounts of data accumulating in areas such as genomics and proteomics, biology and biomedicine have come to rely increasingly on the use of computational methods in their research. One of the most impressive and influential developments in this regard is the so-called Gene Ontology (GO), which is being developed as part of the effort to produce controlled vocabularies for shared use across different biological domains within the framework of the Open Biological Ontologies project. We take GO as our test case in what follows, not only because it has proved so successful in serving as a common reference system for a variety of groups working at the forefront of biomedical research, but also because, as we shall see, it suffers from a series of problems which are characteristic of almost all current ontologies used in bioinformatics. 1 The Gene Ontology Consortium, “Gene Ontology: Tool for the Unification of Biology. Nature Genetics, 25 (2000), 25-29. See also: http://www.geneontology.org. 2 http://obo.sourceforge.net.