Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between philosophical ontology and applied (scientific) ontology that have been advanced in the history of philosophy. Adoption of a strong participation model for the philosophical ontologist in science is urged, and requirements and consequences of the participation model are explored. This approach provides both a principled view and justification of the role of the philosophical ontologist in contemporary empirical science as well as guidelines for integrating philosophers and philosophical contributions into the practice of science.