Biology:MetaNetX
 | |
|---|---|
| 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 centre | 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 application | Import and map models MNXref ID mapper |
| Miscellaneous | |
| Software 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
- ↑ "MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks". Bioinformatics 29 (6): 815-816. Mar 2013. doi:10.1093/bioinformatics/btt036. PMID 23357920.
- ↑ "Reconciliation of metabolites and biochemical reactions for metabolic networks". Briefings in Bioinformatics 15 (1): 123-135. Jan 2014. doi:10.1093/bib/bbs058. PMID 23172809.
- ↑ "MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks". Nucleic Acids Research 44 (D1): D523–D526. Jan 2016. doi:10.1093/nar/gkv1117. PMID 26527720.
- ↑ "MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models". Nucleic Acids Research 49 (D1): D570-D574. Jan 2021. doi:10.1093/nar/gkaa992. PMID 33156326.
 |  |
