BIOINFORMATICS Capturing expert knowledge with argumentation: a case study in bioinformatics

Motivation: 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, addi-tional data and statistical analysis. Often the process is laborious, goes unrecorded, and may be biased. Argumentation is an establis-hed 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 to 10 percentage points is achieved. This technique can be applied to a wide range of bioinformatic tools. Availability: Example public server and benchmarking data availabl