RT Journal Article
SR Electronic
T1 GROOLS: reactive graph reasoning for genome annotation through biological processes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 117994
DO 10.1101/117994
A1 Jonathan Mercier
A1 Adrien Josso
A1 Claudine Médigue
A1 David Vallenet
YR 2017
UL http://biorxiv.org/content/early/2017/03/18/117994.abstract
AB Motivation High quality functional annotation is essential for understanding the phenotypic consequences encoded in a genome. Despite improvements in bioinformatics methods, millions of sequences in databanks are not assigned reliable functions. The curation of protein functions in the context of biological processes is a way to improve and validate their annotation.Results We developed an expert system using paraconsistent logic, named GROOLS (Genomic Rule Object-Oriented Logic System), that assists biocurators in functional annotation of proteins. GROOLS evaluates the completeness and the consistency of predicted functions through biological processes like metabolic pathways. At the end of the reasoning, conclusions are assigned to biological process components and highlight confirmed/missing predictions and potential conflicts with expectations (e.g. growth phenotype experiments). Results on 14 microbial organisms are presented.Availability GROOLS is implemented as a standalone Java application. GROOLS is free open source software distributed under CeCILL license and can be downloaded from https://github.com/Grools.Supplementary information Detailed results are available at https://www.genoscope.cns.fr/agc/groolshttp://dx.doi.org/XX.XXXXXX