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Argumentation to Represent and Reason over Biological Systems

  • Adam Wyner
  • Luke Riley
  • Robert Hoehndorf
  • Samuel Croset
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7451)

Abstract

In systems biology, networks represent components of biological systems and their interactions. It is a challenge to efficiently represent, integrate and analyse the wealth of information that is now being created in biology, where issues concerning consistency arise. As well, the information offers novel methods to explain and explore biological phenomena. To represent and reason with inconsistency as well as provide explanation, we represent a fragment of a biological system and its interactions in terms of a computational model of argument and argumentation schemes. Process pathways are represented in terms of an argumentation scheme, then abstracted into a computational model for evaluation, yielding sets of ‘consistent’ arguments that represent compatible biological processes. From the arguments, we can extract the corresponding processes. We show how the analysis supports explanation and systematic exploration in a biology network.

Keywords

argumentation systems biology computational methods 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Adam Wyner
    • 1
  • Luke Riley
    • 1
  • Robert Hoehndorf
    • 2
  • Samuel Croset
    • 3
  1. 1.Department of Computer ScienceUniversity of LiverpoolLiverpoolUK
  2. 2.Department of GeneticsUniversity of CambridgeCambridgeUK
  3. 3.European Bioinfomatics InstituteCambridgeUK

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