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In this paper, we describe the IS-BioBank (Integrated Semantic Biological Data Bank) proposal. It consists of the realization of a framework for enabling the interoperability among different biological data sources and for ultimately supporting expert users in the complex process of extraction, navigation and visualization of the precious knowledge hidden in such a huge quantity of data. In this framework, a key role has been played by the Connectivity Map, a databank which relates diseases, physiological processes, and the action of drugs. 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