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Bernard T, Bridge A, Morgat A, et al. Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform. 2012;15(1):123-35doi: 10.1093/bib/bbs058.
Bernard, T., Bridge, A., Morgat, A., Moretti, S., Xenarios, I., & Pagni, M. (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in bioinformatics, 15(1), 123-35. https://doi.org/10.1093/bib/bbs058
Bernard, Thomas, et al. "Reconciliation of metabolites and biochemical reactions for metabolic networks." Briefings in bioinformatics vol. 15,1 (2014): 123-35. doi: https://doi.org/10.1093/bib/bbs058
Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M. Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform. 2014 Jan;15(1):123-35. doi: 10.1093/bib/bbs058. Epub 2012 Nov 19. PMID: 23172809; PMCID: PMC3896926.
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Brief Bioinform. 2014 Jan;15(1):123-35. doi: 10.1093/bib/bbs058. Epub 2012 Nov 19.

Reconciliation of metabolites and biochemical reactions for metabolic networks.

Briefings in bioinformatics

Thomas Bernard, Alan Bridge, Anne Morgat, Sébastien Moretti, Ioannis Xenarios, Marco Pagni

Affiliations

  1. Corresponding author. Marco Pagni.

PMID: 23172809 PMCID: PMC3896926 DOI: 10.1093/bib/bbs058

Abstract

Genome-scale metabolic network reconstructions are now routinely used in the study of metabolic pathways, their evolution and design. The development of such reconstructions involves the integration of information on reactions and metabolites from the scientific literature as well as public databases and existing genome-scale metabolic models. The reconciliation of discrepancies between data from these sources generally requires significant manual curation, which constitutes a major obstacle in efforts to develop and apply genome-scale metabolic network reconstructions. In this work, we discuss some of the major difficulties encountered in the mapping and reconciliation of metabolic resources and review three recent initiatives that aim to accelerate this process, namely BKM-react, MetRxn and MNXref (presented in this article). Each of these resources provides a pre-compiled reconciliation of many of the most commonly used metabolic resources. By reducing the time required for manual curation of metabolite and reaction discrepancies, these resources aim to accelerate the development and application of high-quality genome-scale metabolic network reconstructions and models.

Keywords: cheminformatics; data integration; data interoperability; metabolic networks; metabolic resources

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