 | |
| Content | |
|---|---|
| Description | Unified namespace for metabolites and biochemical reactions in the context of metabolic models |
| Data types captured | Small chemical compounds, biochemical reactions, cellular compartments, genome-scale metabolic models |
| Contact | |
| Research center |
SIB Swiss Institute of Bioinformatics Vital-IT group |
| Primary citation | PMID 33156326 |
| Release date | June 2011 |
| Access | |
| Website |
www |
| Download URL |
www |
| Sparql endpoint |
rdf |
| Tools | |
| Web |
Import and map models MNXref ID mapper |
| Miscellaneous | |
| 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:
References
- ^ Ganter M, Bernard T, Moretti S, Stelling S, Pagni M (Mar 2013). "MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks". Bioinformatics. 29 (6): 815–816. doi: 10.1093/bioinformatics/btt036. PMC 3597148. PMID 23357920.
- ^ Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M (Jan 2014). "Reconciliation of metabolites and biochemical reactions for metabolic networks". Briefings in Bioinformatics. 15 (1): 123–135. doi: 10.1093/bib/bbs058. PMC 3896926. PMID 23172809.
- ^ Moretti S, Martin O, Van Du Tran T, Bridge A, Morgat A, Pagni M (Jan 2016). "MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks". Nucleic Acids Research. 44 (D1): D523–D526. doi: 10.1093/nar/gkv1117. PMC 4702813. PMID 26527720.
- ^ Moretti S, Van Du Tran T, Mehl F, Ibberson M, Pagni M (Jan 2021). "MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models". Nucleic Acids Research. 49 (D1): D570–D574. doi: 10.1093/nar/gkaa992. PMC 7778905. PMID 33156326.