Ontologies are more and more used in clinical informatics in different settings and supporting different functionalities. Most experts see the role of ontologies as operating in a black box and being invisible for the end-user. With respect to some of the systems that have recently been developed this is only partly possible. Therefore, we provide a methodology to create an end-user perspective on a clinical ontology. This will foster participation of the clinical expert in both ontology exploitation and ontology maintenance. This methodology does not only provide the basis for a better integration of the experts into the ontology-based system, but it can be used to support patient empowerment by helping the patient to understand the content that is stored and partake in its management.