The course will investigate ontologies appropriate for biological mechanisms. 'Ontology' in this context may be defined as "a controlled vocabulary for representing the types of entities in a given domain" (Arp, Smith, Spear 2015, p. ix). Rather than deep issues about metaphysics, the goal is more practical: to develop vocabulary for use in a knowledge base suitable for computational applications, such as computational knowledge discovery. My current research is in computational biology and artificial intelligence and our research group is devising an ontology for representing disease mechanisms; hence, my interest in considering more abstract principles for building ontologies in this course. Philosophers are now engaged in considering the principles for building good ontologies and this is the more general topic we will consider. Barry Smith, one of the authors of one of our textbooks, is such a philosopher.
The course begins with an introduction to the new mechanistic philosophy of science, with which I've been engaged for nearly 20 years. The next section of the course will be a study of formal principles for building an ontology, with a focus on examples of current bio-ontologies, such as GO, the gene ontology. The problematic to be addressed is to investigate ontologies for disease mechanism representations, although students will be encouraged to find, evaluate, and maybe construct ontologies in their particular fields of interest.
The final project for the philosophy students in the course will be to write a paper on mechanisms in an area of interest to them (whether or not it involves ontology questions). Graduate students from biology, computational biology, bioinformatics, science education or other fields should discuss an appropriate final project with the instructor. Philosophy graduate students should know that they should plan to organize their schedule so as to complete their final paper by the end of the semester; an incomplete is not an option. Graduate students who took my Spring 2015 Phil 858J, Mechanisms: Discovery and Explanation, will be thoroughly prepared for the first month of this seminar, but material on ontology and disease mechanisms will be new.
(1) Craver, Carl F. and Lindley Darden (2013), In Search of Mechanisms: Discoveries across the Life Sciences. Chicago, IL: University of Chicago Press.