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

Bioinformatics, vol. 37, pp. 3974–3975

Abstract

MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: DEMETER and tutorials are freely available at https://github.com/opencobra. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors 4

1. Almut Heinken

   Ollscoil na Gaillimhe – University of Galway

   Affiliation as printed

   Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland

   School of Medicine, National University of Galway , H91 TK33 Galway, Ireland

   School of Medicine, National University of Galway, H91 TK33 Galway, Ireland

2. Stefanía Magnúsdóttir

   University Medical Center Utrecht

   Affiliation as printed

   Center for Molecular Medicine, University Medical Center Utrecht , 3584 CX Utrecht, The Netherlands

   ‡Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands

3. Ronan M. T. Fleming Aachen Leiden Academic Centre for Drug Research

   Leiden University · Ollscoil na Gaillimhe – University of Galway

   Affiliation as printed

   Leiden Academic Centre for Drug Research, Leiden University , 2333 CC Leiden, The Netherlands

   School of Medicine, National University of Galway , H91 TK33 Galway, Ireland

   Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands

   School of Medicine, National University of Galway, H91 TK33 Galway, Ireland

4. Ines Thiele corresponding

   Ollscoil na Gaillimhe – University of Galway · University College Cork · APC Microbiome Institute

   Affiliation as printed

   APC Microbiome Ireland, University College Cork , T12 K8AF Cork, Ireland

   Division of Microbiology, National University of Galway , H91 TK33 Galway, Ireland

   Ryan Institute, National University of Galway , H91 TK33 Galway, Ireland

   School of Medicine, National University of Galway , H91 TK33 Galway, Ireland

   National University of Ireland, Galway#TAB#