Flow cytometry has become a technique of paramount importance in the armamentarium of the scientist in such domains as immunogenetics. In the PENGUIN project, we are currently developing the architecture for an expert- database-system to facilitate the design of flow-cytometry experiments. This paper describes the core of this architecture—a methodology for managing complex biomedical information in an extended relational framework. More specifically, we exploit the structural model to enhance relational databases with structuring and manipulation tools that take more semantics into account and provide the user with an appropriate level of abstraction. We present specific applications of the structural model to database design, schema management, data retrieval and browsing, and integrity maintenance.