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Bioinformatics 2008 24(13):i304-i312; doi:10.1093/bioinformatics/btn157
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Towards the use of argumentation in bioinformatics: a gene expression case study

Kenneth McLeod 1,* and Albert Burger 1,2

1Department of Computer Science, Heriot-Watt University and 2MRC Human Genetics Unit, Edinburgh, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: Due to different experimental setups and various interpretations of results, the data contained in online bioinformatics resources can be inconsistent, therefore, making it more difficult for users of these resources to assess the suitability and correctness of the answers to their queries. This work investigates the role of argumentation systems to help users evaluate such answers. More specifically, it looks closely at a gene expression case study, creating an appropriate representation of the underlying data and series of rules that are used by a third-party argumentation engine to reason over the query results provided by the mouse gene expression database EMAGE.

Results: A prototype using the ASPIC argumentation engine has been implemented and a preliminary evaluation carried out. This evaluation suggested that argumentation can be used to deal with inconsistent data in biological resources.

Availability: The ASPIC argumentation engine is available from http://www.argumentation.org. EMAGE gene expression data can be obtained from http://genex.hgu.mrc.ac.uk. The argumentation rules for the gene expression example are available from the lead author upon request.

Contact: kcm1{at}hw.ac.uk


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