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Automating the process of information retrieval and integration of heterogeneous biological data is complex and difficult. This paper describes an approach to solve this problem by using XML technologies such as XML Schema and an XML-based active rules system. Current limitations of active rule system for XML databases are discussed. We then propose a template for defining rules that is consistent with the current XQuery specification, a defacto standard language for querying XML data. Finally, an example scenario is used to illustrate how these techniques can come together in integrating heterogeneous biological data sources.