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Efficient XML data management for systems biology: Problems, tools and future vision

Authors:
Lena Strömbäck
David Hall
Mikael Åsberg
Stefan Schmidt

Keywords: XML; XQuery; hybrid XML management; graph processing; systems biology

Abstract:
Recently, XML has become a very popular representation format for exchange of data within systems biology. This has made large amounts of XML data available on the Internet and there is a need for tools to easily and efficiently manage this data. In this paper we give an overview of existing standards and analyze the situation. We describe two tools that have been developed to provide and experiment with data management for XML standardized data. We evaluate the efficiency for each of the tools, show that they provide more efficient data management and make a proposal for a future combined solution. The paper is an extended version of [1] where we put the work in a larger context of efficient XML data management for systems biology.

Pages: 217 to 233

Copyright: Copyright (c) to authors, 2009. Used with permission.

Publication date: December 1, 2009

Published in: journal

ISSN: 1942-2628