One of the hardest tasks in any healthcare application is the management of knowledge. Organisational information as well as medical concepts should be represented in an appropriate way in order to improve interoperability among existing systems, to allow the implementation of knowledge-based intelligent systems, or to provide high level support to healthcare professionals. This paper proposes the inclusion of an especially designed ontology into an agent-based medical platform called HeCaSe2. The ontology has been constructed as an external resource, allowing agents to coordinate complex activities defined in any clinical guideline.