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

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@hw.ac.uk

Argudas: lessons for argumentation in biology based on a gene expression use case

“…Argudas is an evolution of the work described previously, and in [14-16]. In the former work two prototypes were developed, see Figure 1.…”

Argumentation to Represent and Reason over Biological Systems

“…In a series of papers, [18], [16], and [17] present an approach to and implementation of argumentation concerning biomolecular pathways. In terms of general subject area and the application of argumentation, their work and that presented here are very closely related.…”

Argudas: arguing with gene expression information

“…M c Leod et al [13] describes an early system designed to tackle the above problems. Essentially, this system allowed a user to enquire if a gene was expressed in a particular tissue from an individual Theiler Stage.…”

“…Arguments were created by the ASPIC argumentation engine using the rules, and biological facts (information pulled dynamically at runtime from EMAGE and GXD). In M c Leod et al [13] the arguments were converted back into natural language and presented to the user as that is the presentation mechanism the expert deemed most suitable. Figure 1 part A shows a screenshot of the results page: two arguments are displayed using one of ASPIC's in-built presentation mechanisms.…”