Personnel involved with conducting complex clinical research employ a myriad of software applications that meet the demands of managing the research. In the domain of clinical trials that are performed as part of research, software applications vary widely in complexity, are generally autonomous, use very distinct trial knowledge representations, and generate enormous amount of data during the course of the research. Integration of the varied applications to share the domain semantics becomes vital to improve the efficiencies of trial data collection and to ensure the quality of collected data. We have built Epoch, a knowledge-base framework to support the management of clinical trials. We developed a set of ontologies that serves as a central knowledge resource of clinical trial knowledge. We present knowledge transformation methods that we have developed to extract out trial-specific configurations for each of the myriad trial-management and data-analytic applications that a re used in a research enterprise. We have adapted our methods for the Immune Tolerance Network, an international collaboration of scientists and clinicians studying immune-mediated diseases. Our initiative uses semantic technologies to provide a consistent basis for software applications to generate and analyze clinical research data.
