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Reconciliation of metabolites and biochemical reactions for metabolic networks
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 database...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896926/ https://www.ncbi.nlm.nih.gov/pubmed/23172809 http://dx.doi.org/10.1093/bib/bbs058 |
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author | Bernard, Thomas Bridge, Alan Morgat, Anne Moretti, Sébastien Xenarios, Ioannis Pagni, Marco |
author_facet | Bernard, Thomas Bridge, Alan Morgat, Anne Moretti, Sébastien Xenarios, Ioannis Pagni, Marco |
author_sort | Bernard, Thomas |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3896926 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-38969262014-01-21 Reconciliation of metabolites and biochemical reactions for metabolic networks Bernard, Thomas Bridge, Alan Morgat, Anne Moretti, Sébastien Xenarios, Ioannis Pagni, Marco Brief Bioinform Papers 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. Oxford University Press 2014-01 2012-11-19 /pmc/articles/PMC3896926/ /pubmed/23172809 http://dx.doi.org/10.1093/bib/bbs058 Text en © The Author 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Papers Bernard, Thomas Bridge, Alan Morgat, Anne Moretti, Sébastien Xenarios, Ioannis Pagni, Marco Reconciliation of metabolites and biochemical reactions for metabolic networks |
title | Reconciliation of metabolites and biochemical reactions for metabolic networks |
title_full | Reconciliation of metabolites and biochemical reactions for metabolic networks |
title_fullStr | Reconciliation of metabolites and biochemical reactions for metabolic networks |
title_full_unstemmed | Reconciliation of metabolites and biochemical reactions for metabolic networks |
title_short | Reconciliation of metabolites and biochemical reactions for metabolic networks |
title_sort | reconciliation of metabolites and biochemical reactions for metabolic networks |
topic | Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896926/ https://www.ncbi.nlm.nih.gov/pubmed/23172809 http://dx.doi.org/10.1093/bib/bbs058 |
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