Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (65)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Achard, F.
Right arrow Articles by Barillot, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Achard, F.
Right arrow Articles by Barillot, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Brief BioinformHome page
P. Romano
Automation of in-silico data analysis processes through workflow management systems
Brief Bioinform, January 1, 2008; 9(1): 57 - 68.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Eccher and C. Priami
Design and implementation of a tool for translating SBML into the biochemical stochastic {pi}-calculus
Bioinformatics, December 15, 2006; 22(24): 3075 - 3081.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
G. M. Saadawi and J. H. Harrison Jr
Definition of an XML Markup Language for Clinical Laboratory Procedures and Comparison with Generic XML Markup
Clin. Chem., October 1, 2006; 52(10): 1943 - 1951.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Sroka, G. Kaczor, J. Tyszkiewicz, and A. M. Kierzek
XQTav: an XQuery processor for Taverna environment
Bioinformatics, May 15, 2006; 22(10): 1280 - 1281.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. Stromback and P. Lambrix
Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX
Bioinformatics, December 15, 2005; 21(24): 4401 - 4407.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Yun, D.-Y. Lee, J. Jeong, S. Lee, and S. Y. Lee
MFAML: a standard data structure for representing and exchanging metabolic flux models
Bioinformatics, August 1, 2005; 21(15): 3329 - 3330.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. He, R. R. Vines, A. R. Wattam, G. V. Abramochkin, A. W. Dickerman, J. D. Eckart, and B. W. S. Sobral
PIML: the Pathogen Information Markup Language
Bioinformatics, January 1, 2005; 21(1): 116 - 121.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
J. E. Stajich, D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz, C. Dagdigian, G. Fuellen, J. G.R. Gilbert, I. Korf, H. Lapp, et al.
The Bioperl Toolkit: Perl Modules for the Life Sciences
Genome Res., October 1, 2002; 12(10): 1611 - 1618.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.