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Bioinformatics Vol. 17 no. 2 2001
Pages 115-125
© 2001 Oxford University Press

Review

XML, bioinformatics and data integration

Frédéric Achard 1,3, Guy Vaysseix 1,2 and Emmanuel Barillot 1,2,*

1 CRI Infobiogen, 523 place des terrasses de l’agora, 91000 Evry, France
2 Généthon, 1 bis rue de l’Internationale, 91000 Evry, France

Received on June 9, 2000 ; revised on September 20, 2000 ; accepted on October 31, 2000

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{at}infobiogen.fr

* To whom correspondence should be addressed.

3 Present address: Cereon Genomics, 45 Sidney St, Cambridge, MA 02139, USA.


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