We present the BioMediator (www.biomediator.org) system and the process of executing queries on it. The system was designed as a tool for posing queries across semantically and syntactically heterogeneous data particularly in the biological arena. We use examples from researchers at the University of Washington, and the University of Missouri-Columbia, to discuss the BioMediator system architecture, query execution, modifications to the system to support the queries, and summarize our findings and our future directions. Finally, we discuss the system's flexibility and generalized approach and give examples of how the system can be extended for a variety of objectives.