MetaNetX explained

MetaNetX
Description:	Unified namespace for metabolites and biochemical reactions in the context of metabolic models
Scope:	Small chemical compounds, biochemical reactions, cellular compartments, genome-scale metabolic models
Center:	SIB Swiss Institute of Bioinformatics Vital-IT group
Pmid:	33156326
Released:	June 2011
Webapp:	Import and map models MNXref ID mapper
License:	CC BY 4.0
Version:	4.4

MetaNetX is a database maintained by the SIB Swiss Institute of Bioinformatics for the automated model construction, and the genome annotation for large-scale metabolic networks. MetaNetX provides a number of tools to access, analyse and manipulate metabolic networks.^[1]

MetaNetX provides a bunch of pre-mapped metabolic models.

To ease model comparison, MetaNetX has developed a resource to unify metabolites and biochemical reactions in the context of metabolic models. This unified namespace is called MetaNetX/MNXref.^{[2] [3] [4]}

MNXref reconciles chemical compounds by structural similarity and biochemical reaction context. Then reconciles biochemical reactions on the basis of the chemical compound reconciliation in an iterative way. Each reconciled group of chemical compounds, biochemical reactions and cellular compartments is a bag of similar items. MNXref sets a referent for each group.

MetaNetX allows search in MNXref by chemical compounds, biochemical reactions and cellular compartments.

Currently, MetaNetX/MNXref reconciles those resources:

• BiGG
• ChEBI
• enviPath
• HMDB
• GO
• KEGG
• LipidMaps
• MetaCyc
• Reactome
• Rhea
• SABIO-RK
• SwissLipids
• The SEED

Notes and References

1. Ganter M, Bernard T, Moretti S, Stelling S, Pagni M . MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks . Bioinformatics . 29 . 6 . 815-816 . Mar 2013 . 23357920 . 10.1093/bioinformatics/btt036 . 3597148 . free .
2. Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M . Reconciliation of metabolites and biochemical reactions for metabolic networks . Briefings in Bioinformatics . 15 . 1 . 123-135 . Jan 2014 . 23172809 . 10.1093/bib/bbs058 . 3896926 . free .
3. Moretti S, Martin O, Van Du Tran T, Bridge A, Morgat A, Pagni M . MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks . Nucleic Acids Research . 44 . D1 . D523–D526 . Jan 2016 . 26527720 . 10.1093/nar/gkv1117 . 4702813 . free .
4. Moretti S, Van Du Tran T, Mehl F, Ibberson M, Pagni M . MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models . Nucleic Acids Research . 49 . D1 . D570-D574 . Jan 2021 . 33156326 . 10.1093/nar/gkaa992 . 7778905 . free .