title: Capturing expert knowledge with argumentation: a case study in bioinformatics.
abstract: BACKGROUND
  The output of a bioinformatic tool such as BLAST must usually be interpreted by an expert before reliable conclusions can be drawn. This may be based upon the expert's experience, additional data and statistical analysis. Often the process is laborious, goes unrecorded and may be biased. Argumentation is an established technique for reasoning about situations where absolute truth or precise probability is impossible to determine.
  
  
  RESULTS
  We demonstrate the application of argumentation to 3D-PSSM, a protein structure prediction tool. The expert's interpretation of results is represented as an argumentation framework. Given a 3D-PSSM result, an automated procedure constructs arguments for and against the conclusion that the result is a good predictor of protein structure. In addition to capturing the unique expertise of the author of 3D-PSSM for distribution to users, an improvement in recall of 5-10 percentage points is achieved. This technique can be applied to a wide range of bioinformatic tools.
  
  
  BACKGROUND
  Example public server and benchmarking data are available at http://www.sbg.bio.ic.ac.uk/~brj03/argumentation/paper/. Source code available on request.
authors.affiliation: Division of Molecular Biosciences, Imperial College, London SW7 2AZ, UK.
authors.forename: Benjamin R
authors.initials: BR
authors.lastname: Jefferys
authors.forename: Lawrence A
authors.initials: LA
authors.lastname: Kelley
authors.forename: Marek J
authors.initials: MJ
authors.lastname: Sergot
authors.forename: John
authors.initials: J
authors.lastname: Fox
authors.forename: Michael J E
authors.initials: MJ
authors.lastname: Sternberg
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D005103:Expert Systems; D008956:Models, Chemical; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins