Today, experiments like microarrays and other high-throughput methods generate a large number of life sciences data. Biologists need to be supported in their research by tools and applications that can analyze and interpret experimental data while considering external data sources or data from experiments of other researchers. Moreover, relationships and interactions between different data sets and biomedical domains have to be detected and represented in a clear and understandable manner. These questions are some of the major challenges in bioinfomatics. Therefore, we present DAWIS-M.D., a platform-independent data warehouse system for metabolic data. This data warehouse information system provides an integrated and consistent view of large scale biomedical data. DAWIS-M.D. is a publicly available web-based system that integrates data from 11 different biomedical databases.