90:4 October 2007
Biomedical Ontologies 

Advisory Editor: Steffen Schulze-Kremer

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about the biology and chemistry of life with an eye to medical applications. Ontologies have come to play an indispensable part in this development, with ambitious projects such as the Gene Ontology™ attempting to produce controlled vocabularies for the description of biological phenomena that can be applied in consistent fashion across a range of different disciplines. Biomedical ontologies seek both to classify the entities within given domains and also to specify the types of relations between these entities. In this, however, they encounter problems familiar to philosophers, problems having to do with the proper handling of types and tokens, of continuants and occurrents, of change and causality. They need to confront also problematic matters such as the proper treatment of information, expression, function, pattern, system and the like, which play an important role in the life sciences. The present issue of The Monist is designed to serve as a forum within which biologists and philosophers can address such problems in a way that is both philosophically rigorous and of practical significance.

Table of Contents:

Michael T. Ghiselin and Olaf Breidbach

The Search for the Basis of Natural Classification

Stefan Schulz and Ingvar Johansson

Continua in Biological Systems

Russ Altman

Ontological Issues in Pharmacogenomics

Ludger Jansen

Tendencies and Other Realizables in Medical Information Sciences

Neil Williams

The Factory Model of Disease

Christopher J. O. Baker, Robert H. Warren, Volker Haarslev, Greg Butler

The Ecology of Ontologies in the Public Domain