MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models

MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular att...

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Detalles Bibliográficos
Autores principales: Moretti, Sébastien, Tran, Van Du T, Mehl, Florence, Ibberson, Mark, Pagni, Marco
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Database Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778905/
https://www.ncbi.nlm.nih.gov/pubmed/33156326
http://dx.doi.org/10.1093/nar/gkaa992
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author Moretti, Sébastien
Tran, Van Du T
Mehl, Florence
Ibberson, Mark
Pagni, Marco
author_facet Moretti, Sébastien
Tran, Van Du T
Mehl, Florence
Ibberson, Mark
Pagni, Marco
author_sort Moretti, Sébastien
collection PubMed
description MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).
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spelling pubmed-77789052021-01-06 MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models Moretti, Sébastien Tran, Van Du T Mehl, Florence Ibberson, Mark Pagni, Marco Nucleic Acids Res Database Issue MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org). Oxford University Press 2020-11-06 /pmc/articles/PMC7778905/ /pubmed/33156326 http://dx.doi.org/10.1093/nar/gkaa992 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Moretti, Sébastien
Tran, Van Du T
Mehl, Florence
Ibberson, Mark
Pagni, Marco
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
title MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
title_full MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
title_fullStr MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
title_full_unstemmed MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
title_short MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
title_sort metanetx/mnxref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778905/
https://www.ncbi.nlm.nih.gov/pubmed/33156326
http://dx.doi.org/10.1093/nar/gkaa992
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