The expansion of clinical information systems and the reduction in computing costs have led to an explosion of patient data available for reuse. However, this data is rarely combined and analyzed in an integrated manner. The DebugIT project is a large-scale integrating project funded within the 7th EU Framework Programme (FP7). The main objectives of the project are to build IT tools that should have significant impacts for the monitoring and the control of infectious diseases and antimicrobial resistances in Europe; this will be realized by building a technical and semantic infrastructure able to a) share heterogeneous clinical data sets from different hospitals in different countries, with different languages and legislations; b) analyze large amounts of this clinical data with advanced multi-modal data mining; c) apply the obtained knowledge for clinical decisions and outcome monitoring. The concepts and architecture underlying this project are discussed.