GROOLS (Genomic Rule Oriented Object Logic System) is a bioinformatics software that helps biologists in the evaluation of genome functional annotation through biological processes like metabolic pathways.
GROOLS is an expert system that uses paraconsistent logic. It evaluates the completeness and the consistency of predicted functions through biological processes like metabolic pathways. Using a generic and hierarchical representation of knowledge, biological processes are modeled in a graph from which observations (i.e. predictions and expectations) are propagated by rules. At the end of the reasoning, conclusions are assigned to biological process components and highlight uncertainties and inconsistencies.
Publication: GROOLS: reactive graph reasoning for genome annotation through biological processes. J Mercier, A Josso, C Medigue, D Vallenet. BMC bioinformatics 19 (1), 132
To download the software: github.com/Grools/grools-application
Results overview on 14 prokaryotic organisms: www.genoscope.cns.fr/agc/grools