Clinical trials are formal patient studies that serve as the gold standard method for establishing the efficacy of medical treatments. There is an enormous requirement to specify the knowledge used at all stages of clinical trials - including planning, implementation, and analysis - so that they can be faithfully executed by a clinical research organization. We are building Epoch, a knowledge-based system, to help a large research consortium, the Immune Tolerance Network (ITN), undertake trials to advance new therapeutics in immune-mediated disorders. We are currently targeting two application areas essential to the successful implementation of a trial: (1) tracking study participants as they advance through a study, and (2) tracking biological specimens as they are processed at laboratories. In this paper, we discuss our use of the Web Ontology Language (OWL) to create a suite of ontologies that conceptualize the clinical trial domain and show how they can inform our system. We show that our ontological framework provides a stable, consistent platform to define, maintain, and distribute the knowledge requirements used in clinical trial management.