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Briefings in Bioinformatics Advance Access originally published online on October 29, 2008
Briefings in Bioinformatics 2009 10(1):11-23; doi:10.1093/bib/bbn045
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis

Mohamed Radhouene Aniba, Sophie Siguenza, Anne Friedrich, Frédéric Plewniak, Olivier Poch, Aron Marchler-Bauer and Julie Dawn Thompson

Corresponding author. Julie D. Thompson, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), F-67400 Illkirch, France. Tel: +33 388653200; Fax: +33 388653201; E-mail: julie{at}igbmc.fr

The traditional approach to bioinformatics analyses relies on independent task-specific services and applications, using different input and output formats, often idiosyncratic, and frequently not designed to inter-operate. In general, such analyses were performed by experts who manually verified the results obtained at each step in the process. Today, the amount of bioinformatics information continuously being produced means that handling the various applications used to study this information presents a major data management and analysis challenge to researchers. It is now impossible to manually analyse all this information and new approaches are needed that are capable of processing the large-scale heterogeneous data in order to extract the pertinent information. We review the recent use of integrated expert systems aimed at providing more efficient knowledge extraction for bioinformatics research. A general methodology for building knowledge-based expert systems is described, focusing on the unstructured information management architecture, UIMA, which provides facilities for both data and process management. A case study involving a multiple alignment expert system prototype called AlexSys is also presented.

Keywords: expert system, knowledge-based system, data integration, UIMA, AlexSys, multiple sequence alignment

Submitted: July 16, 2008. Received (in revised form): October 2, 2008.


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