The medical milieu is an open environment characterized by a variety of distributed, heterogeneous and autonomous information resources. Coordination, cooperation and exchange of information is important to the medical community. Efficient storage and acquisition of medical knowledge requires structured and standardized organization of data. We design a new ontology, called Generic Human Disease Ontology (GHDO), for the representation of knowledge regarding human diseases. The concepts of the GHDO ontology are organized into the following four 'dimensions': Disease Types, Symptoms, Causes and Treatments. We align and merge existing ontologies against the four dimensions of GHDO. The designed ontology makes our query system suitable for different user categories. The process of problem decomposition into smaller sub-problems within a multi-agent system becomes much easier as well. We also design a multi-agent system framework over different information resources. The multi-agent system uses the common GHDO ontology for query formulation, information retrieval and information integration. This intelligent dynamic system provides opportunities to collect information from multiple information resources, to share data efficiently and to integrate and manage scientific results in a timely manner.