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This work presents a customizable software framework that supports the analysis of correlations between genotype and phenotype within an integrated database in the context of metabolic disorders. The basis for the examination of relations between genotypes and phenotypes is the information from different life science data sources, merged by a mediator-based system in an integrated database. A graphical Web interface enables user queries to the integrated data and the trace of connections to corresponding data objects in different information domains. As a result of this work, a Web-based prototype of the system is presented. In the context of an example scenario, the framework was used to integrate clinical and molecular biology data for rare metabolic diseases. The framework offers software tools to integrate almost any life science data and to prepare the content for user-specific presentation.