Reviewhybrid2001

XML, bioinformatics and data integration

Frédéric Achard · Guy Vaysseix · Emmanuel Barillot

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Scientific Computing and Data Management Genomics and Phylogenetic Studies Genetics, Bioinformatics, and Biomedical Research

Abstract

Abstract Motivation: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML for data interchange between databases and other sources of data. Finally the discussion is illustrated by a test case of a pedigree data model in XML. Contact: Emmanuel.Barillot@infobiogen.fr * To whom correspondence should be addressed. 3 Present address: Cereon Genomics, 45 Sidney St, Cambridge, MA 02139, USA.

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