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.