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Possibilities and Challenges Using XML Technology for Storage and Integration of Molecular Interactions

The amount of data emerging from experiments on molecular and protein interactions is rapidly growing. It is of high importance to understand these datasets, putting them together to meaningful pathways describing some aspects of the cell physiology. Currently, there is a big interest in XML representations of protein interaction and molecular pathways. New standards, SBML, PSI MI and BioPAX are under development and it is of high importance to build tools for easy integration and analysis of data represented in these standards. There are currently two main approaches for storage of data represented within XML, one is to base the tools directly on XML while the other is to translate the information into a relational database. In this paper we report on experiments with these approaches for storage and analysis of molecular interaction data represented in the standards. The results give important pointers to the possibility of building easy to use tools