Clinical trials encompass a vast array of studies in treatment, prevention or diagnosis of medical conditions. There is an enormous requirement for knowledge and information management at all stages of the trials – planning, specification, implementation, and analysis. We are building Epoch, a knowledge-based system to manage clinical trials in the Immune Tolerance Network (ITN) in developing new therapeutics in immune-mediated disorders. In the broad spectrum of trial management activities, we are currently targeting two areas that are vital to the successful implementation of a trial – tracking study participants as they advance through the studies, and tracking clinical specimens as they are processed at the trial laboratories. The core of our system is a suite of medical ontologies that conceptualizes the clinical trial domain relevant to our participant and specimen tracking applications. We expect that our ontological solution can provide a stable and consistent platform to support our current and future requirements of clinical trial management.