PT  - JOURNAL ARTICLE
AU  - Jonathan Mercier
AU  - Adrien Josso
AU  - Claudine Médigue
AU  - David Vallenet
TI  - GROOLS: reactive graph reasoning for genome annotation through biological processes
AID  - 10.1101/117994
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 117994
4099  - http://biorxiv.org/content/early/2017/03/18/117994.short
4100  - http://biorxiv.org/content/early/2017/03/18/117994.full
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