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The development of high-throughput genome sequencing and protein structure determination techniques have provided researchers with a wealth of biological data. Integrated analysis of such data is difficult due to the disparate nature of the repositories used to store this biological data and of the software used for its analysis. This paper presents a framework based upon the use of semi-structured database management systems that would provide an integrated interface for the collection, storage and retrieval of biological data from existing repositories and of biological information generated by existing analysis programs. A simple implementation that integrates information from databases and analytical programs is presented as a proof of concept. In particular, this paper focuses on the data transformation, data integration, and the support of active rules for biological data.