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Briefings in Bioinformatics Advance Access originally published online on July 11, 2008
Briefings in Bioinformatics 2008 9(6):493-505; doi:10.1093/bib/bbn029
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

This article appears in the following Briefings in Bioinformatics issue: Special Issue:Database Integration in Life Sciences [View the issue table of contents]

Experience using web services for biological sequence analysis

Heinz Stockinger, Teresa Attwood, Shahid Nadeem Chohan, Richard Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro Fernandes, Robert D. Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurelie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan and Nazim Rahman

Corresponding author. Heinz Stockinger, Swiss Institute of Bioinformatics, Vital-IT Group, Lausanne, Switzerland. Tel: +41 21 692 40 89; Fax: +41 21 692 40 65; E-mail: Heinz.Stockinger{at}isb-sib.ch

Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.

Keywords: web services, SOAP, REST, internet technologies, sequence analysis

Submitted: March 3, 2008. Received (in revised form): June 11, 2008.


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