title: Mechanisms in biomedical ontology.
abstract: The concept of a mechanism has become a standard proposal for explanations in biology. It has been claimed that mechanistic explanations are appropriate for systems biology, because they occupy a middle ground between strict reductionism and holism. Because of their importance in the field a formal ontological description of mechanisms is desirable. The standard philosophical accounts of mechanisms are often ambiguous and lack the clarity that can be provided by a formal-ontological framework. The goal of this paper is to clarify some of these ambiguities and suggest such a framework for mechanisms. Taking some hints from an "ontology of devices" I suggest as a general approach for this task the introduction of functional kinds and functional parts by which the particular relations between a mechanism and its components can be captured.
authors.affiliation: Department of Philosophy, University of Rostock, August-Bebel-Strasse 28, 18051 Rostock, Germany. johannes.roehl@uni-rostock.de.
authors.forename: Johannes
authors.initials: J
authors.lastname: Röhl