DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.

Abstract

Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools do not typically take species-specific experimental and curated genomic data into account. We developed Data-drivEn METabolic nEtwork Refinement (DEMETER), a Constraint-Based Reconstruction and Analysis (COBRA) Toolbox extension, which enables the efficient, simultaneous refinement of thousands of draft genome-scale reconstructions, while ensuring adherence to the quality standards in the field, agreement with available experimental data and refinement of pathways based on manually refined genome annotations. DEMETER and tutorials are freely available at https://github.com/opencobra. Supplementary data are available at Bioinformatics online.