The Role of Foundational Relations in the Alignment of Biomedical Ontologies

Smith, Barry and Rosse, Cornelius (2004) The Role of Foundational Relations in the Alignment of Biomedical Ontologies. In Proceedings, MedInfo 2004, pages pp. 444-448, San Francisco, CA.

Abstract

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities on the basis of explicit definitions. This scheme also provides a template for modeling pathology, physiological function and genotype-phenotype correlations, and it can thus serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and partof relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies.