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. 2021 Jan 8;49(D1):D570-D574.
doi: 10.1093/nar/gkaa992.

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

Sébastien Moretti  1 , Van Du T Tran  1 , Florence Mehl  1 , Mark Ibberson  1 , Marco Pagni  1
Affiliations

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

Sébastien Moretti et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1.
Figure 1.
Example of the progressive reconciliation of five metabolites in four reactions into two metabolites in a single reaction. Three lines of evidence are used successively: (1) identical structures; (2) similar structures in reaction context; (3) structure and symbol pair in reaction context.
Figure 2.
Figure 2.
A status (A, a, b, B) was attributed to every reaction of this simple network, as explained in the text. A reaction status ultimately depends on the whole network topology and the directionality of every reaction.
See this image and copyright information in PMC

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