Part-whole representation and reasoning in formal biomedical ontologies

Objective: Biomedical ontologies are typically structured in a biaxial way, reflecting both a taxonomic (is-a) and a partonomic (part-of) hierarchy. Commonly used biomedical terminologies, which incorporate such distinctions excel in terms of broad coverage but lack a rigid formal foundation. The latter, however, is a prerequisite for automated reasoning. For the biomedical domain, it is not only crucial to cope with ontological dependencies between wholes and their parts but also with specific reasoning patterns which underlie the propagation of roles across partonomic hierarchies. Methods: We scale down part-whole reasoning to subsumption-based taxonomic reasoning within the formal framework of a parsimonious variant of description logics (viz. ALC). Results: We provide a formal basis for ontological engineering in the domain of biomedicine, as far as part-whole relationships are concerned, by addressing typical reasoning patterns encountered in this domain. (c) 2005 Elsevier B.V. All rights reserved.