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

Sébastien Moretti; Van Du T Tran; Florence Mehl; Mark Ibberson; Marco Pagni

doi:10.1093/nar/gkaa992

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

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

Authors

Sébastien Moretti¹, Van Du T Tran¹, Florence Mehl¹, Mark Ibberson¹, Marco Pagni¹

Affiliation

¹ Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.

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).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Curation
Databases, Factual*
Metabolic Networks and Pathways*
Metabolome*
Models, Biological*