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

TL;DR

DEMETER is a tool that automates the simultaneous refinement of thousands of genome-scale reconstructions by integrating experimental data and refined gene annotations, improving accuracy and efficiency.

Contribution

It introduces DEMETER, a COBRA Toolbox extension that automates large-scale curation of genome reconstructions considering species-specific data and annotations.

Findings

Enables efficient refinement of thousands of reconstructions

Ensures adherence to quality standards and experimental data

Refines pathways based on manually curated annotations

Abstract

Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We developed DEMETER, a COBRA Toolbox extension that 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. Availability: DEMETER and tutorials are available at https://github.com/opencobra/cobratoolbox.