Formal ontology for natural language processing and the integration of biomedical databases

The central hypothesis underlying this communication is that the methodology and conceptual rigor of a philosophically inspired formal ontology can bring significant benefits in the development and maintenance of application ontotogies [A. Flett, M. Dos Santos, W. Ceusters, Some Ontology Engineering Procedures and their Supporting Technologies, EKAW2002, 2003]. This hypothesis has been tested in the collaboration between Language and Computing (L & C), a company specializing in software for supporting natural language processing especially in the medical field, and the Institute for Format Ontology and Medical Information Science (IFOMIS), an academic research institution concerned with the theoretical foundations of ontology. In the course of this collaboration L & C's ontology, LinKBase (R), which is designed to integrate and support reasoning across a plurality of external databases, has been subjected to a thorough auditing on the basis of the principles underlying IFOMIS's Basic Format Ontology (BFO) [B. Smith, Basic Formal Ontology, 2002. http://ontology.buffato.edu/bfo]. The goal is to transform a large terminology-based ontology into one with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase (R) are standardized in the framework of first-order logic. In this paper we describe how this principles-based standardization has led to a greater degree of internal coherence of the LinKBase (R) structure, and how it has facilitated the construction of mappings between external databases using LinKBase (R) as translation hub. We argue that the collaboration here described represents a new phase in the quest to solve the so-called "Tower of Babel" problem of ontology integration [F. Montayne, J. Flanagan, Format Ontology: The Foundation for Natural Language Processing, 2003. http: //www.landcgtobat.com/]. (c) 2005 Elsevier Ireland Ltd. All rights reserved.