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Integration of data from heterogeneous sources has been a problem in medicine over decades. In the post genomicera, new opportunities have emerged and created new challenges, e.g. when genotypes and phenotypes have to be associated. We have developed a concept for integrating data from systems in clinical and in research environments, with a specific focus on process support. Our solution is following a mediator based approach, realized in a service-oriented architecture using web services. In order to cope with complexity and changing requirements, and to make early user feedback possible, a tool-based agile software development process has been carried out for building a prototype. Open-source technology has been used for the implementation.