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Briefings in Bioinformatics Advance Access originally published online on December 2, 2007
Briefings in Bioinformatics 2008 9(1):57-68; doi:10.1093/bib/bbm056
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Automation of in-silico data analysis processes through workflow management systems

Paolo Romano

Corresponding author. Paolo Romano, Bioinformatics, Istituto Nazionale per la Ricerca sul Cancro, Largo Rosanna Benzi 10, I-16132, (IST), Genova, Italy. Tel: +39-010-5737288; Fax: +39-010-5737295; E-mail: paolo.romano{at}istge.it

Data integration is needed in order to cope with the huge amounts of biological information now available and to perform data mining effectively. Current data integration systems have strict limitations, mainly due to the number of resources, their size and frequency of updates, their heterogeneity and distribution on the Internet. Integration must therefore be achieved by accessing network services through flexible and extensible data integration and analysis network tools. EXtensible Markup Language (XML), Web Services and Workflow Management Systems (WMS) can support the creation and deployment of such systems. Many XML languages and Web Services for bioinformatics have already been designed and implemented and some WMS have been proposed. In this article, we review a methodology for data integration in biomedical research that is based on these technologies. We also briefly describe some of the available WMS and discuss the current limitations of this methodology and the ways in which they can be overcome.

Keywords: biological data integration, automation of retrieval and analysis processes, XML, web services, workflow management systems, ontologies

Submitted: August 31, 2007. Received (in revised form): October 17, 2007.


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