Biomedical questions are usually complex and regard several different life science aspects. Numerous valuable and he- terogeneous data are increasingly available to answer such questions. Yet, they are dispersedly stored and difficult to be queried comprehensively. We created a Genomic and Proteomic Data Warehouse (GPDW) that integrates data provided by some of the main bioinformatics databases. It adopts a modular integrated data schema and several metadata to describe the integrated data, their sources and their location in the GPDW. Here, we present the Web application that we developed to enable any user to easily compose queries, although complex, on all data integrated in the GPDW. It is publicly available at http://www.bioinformatics.dei.polimi.it/GPKB/. Through a visual interface, the user is only required to select the types of data to be included in the query and the conditions on their values to be retrieved. Then, the Web application leverages the metadata and modular schema of the GPDW to automatically compose an efficient SQL query, run it on the GPDW and show the extracted requested data, enriched with links to external data sources. Performed tests demonstrated efficiency and usability of the developed Web application, and showed its and GPDW relevance in supporting answering biomedical questions, also difficult.