The expansion of biomedical knowledge, reductions in computing costs and spread of IT facilities have led to an explosion of the biomedical electronic data. However, these data are rarely integrated and analysed because of lack of tools. The integration process is complex due to technical and semantic heterogeneity as well as lack of reliability in such distributed system. In addition, for the specific case of biomedical data, privacy is a crucial constraint. This paper presents a pilot system that will be used in the European FP7 DebugIT project to integrate biomedical data from several healthcare centres across Europe.