
Enter one or several terms to search for in MNXref: You can search for chemicals, reactions or compartments A + sign in front of a term will search for this exact term. E.g. MNXM89588, glucose phosphate, +synthase, Golgi

The MNXref namespace

The method to compute the MNXref namespace is described in Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M (2014) Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics 15(1):123-135.

Disclaimer

Except where otherwise noted, the data available from this site are licensed under a Creative Commons Attribution 4.0 International License.
MNXref uses information on cellular compartments, reactions, and metabolites that is sourced from a number of external resources. The licensing agreements of those resources are specified in each of the downloadable files listed below. For each compound, reaction and cellular compartment in the MNXref namespace we indicate which external resource provided the information used in MNXref. Compounds and reactions in the MNXref namespace may be identical to, or differ from, those in the external resource. In either case the data from MNXref may be considered to be subject to the original licensing restrictions of the external resource.

MNXref version 4.1 data sources

Data source name	Data source version
Chemicals
BiGG	2019/10/31
ChEBI	185
enviPath	2017/04/12
HMDB	4.0
KEGG	93.0+/01-30
LipidMaps	2019/10/02
MetaCyc	23.5
Reactome	72
SABIO-RK	2019/09/20
SwissLipids	2020/03/19
The SEED	2019/12/20
Reactions
BiGG	2019/10/31
KEGG	93.0+/01-30
MetaCyc	23.5
Rhea	111
SABIO-RK	2019/09/20
The SEED	2019/12/20
Compartments
BiGG	2019/10/31
CCO	23.5
GO	2019/12/09
The SEED	2019/12/20
Proteins
UniProt	2019_10

Previous releases
Previous releases of the MNXref namespace are available at MNXref FTP.

Files content
All data files are made of TAB-delimited values. Comment lines starting with # appear at the beginning of all files. MNXref 4.0 release notes: Some columns have been reordered or suppressed, with respect to previous releases. The content should be improved and streamlined.

File name	Column content
chem_xref.tsv	The identifier of a chemical compound in an external resource [XREF] The corresponding identifier in the MNXref namespace [MNX_ID] The description given by the external resource [STRING] MNXref 4.0 release notes: The third column (evidence tag for the mapping) was suppressed The descriptions were completed Deprecated identifiers were moved into they own table below
chem_prop.tsv	The identifier of the chemical compound in the MNXref namespace [MNX_ID] The common name of the compound [STRING] The original best resource from where this compound comes from [REFERENCE] The formula of the compound [STRING] The charge of the compound [INTEGER] The mass of the compound [REAL] The standard InChI of the compound [STRING] The standard InChIKey of the compound [STRING] The SMILES of the compound [STRING] MNXref 4.0 release notes: !!! The columns have been reordered !!! Formulas that ends with * are incomplete - there are no R-groups in formulas anymore
chem_depr.tsv	The deprecated identifier [MNX_ID] The replacement identifier [MNX_ID] This happened in this MNXref version [STRING] MNXref 4.0 release notes: This is a new dataset One-to-one, many-to-one (merge) and one-to-many (split) mappings are possible
comp_xref.tsv	The identifier of a sub-cellular compartment in an external resource [XREF] The corresponding identifier in the MNXref namespace [MNX_ID] The description given by the external resource [STRING]
comp_prop.tsv	The identifier of the sub-cellular compartment in the namespace [MNX_ID] The common name of that compartment [STRING] The original best resource from where this compartment comes from [REFERENCE] MNXref 4.0 release notes: The content of this file was drastically simplified/sanitized
comp_depr.tsv	The deprecated identifier [MNX_ID] The replacement identifier [MNX_ID] This happened in this MNXref version [STRING] MNXref 4.0 release notes: This is currently an empty dataset (placeholder) that will be filled in future release
reac_xref.tsv	The identifier of a biochemical reaction in an external resource [XREF] The corresponding identifier in the MNXref namespace [MNX_ID] The biochemical reaction given by the external resource [STRING]
reac_prop.tsv	The identifier of the reaction in the MNXref namespace [MNX_ID] Equation of the reaction in the MNXref namespace (compartmentalized and undirected) [EQUA] The original best resource from where this reaction comes from [REFERENCE] The EC(s) associated to this reaction [STRING] Is the equation balanced with respect to elemental composition and charge [BOOLEAN] Is this a transport reaction[BOOLEAN] MNXref 4.0 release notes: !!! The columns were reordered !!! The column "human readable equation" was suppressed
reac_depr.tsv	The deprecated identifier [MNX_ID] The replacement identifier [MNX_ID] This happened in this MNXref version [STRING] MNXref 4.0 release notes: This is a new dataset One-to-one, many-to-one (merge) and one-to-many (split) mappings are possible

Data types
Type	Specification
MNX_ID	An MNXref identifier starts with the MNX prefix, followed by a single letter indicating the type of object: R for reaction; M for metabolite; C for cellular compartment; D for generic cellular compartment and followed by an integer number, e.g. MNXR96826
REFERENCE	The best external resource identifier. It is made of a database identifier, followed by ':', followed by an entry identifier or an accession number. For example: chebi:28423
XREF	An external resource identifier. It is made of a database identifier, followed by ':', followed by an entry identifier or an accession number. For example: chebi:1234
EQUA	The chemical equation for a reaction is written using the MNXref identifiers for the substrates and products. Non-numeric stoichiometric coefficients (for (de)polymerization reactions) are placed between parentheses. Since MNXref release 3.0, the chemical compounds here are attributed to a generic compartment, and reactions have no direction. It turned out that transport reactions are represented with identical left and right terms, with different generic compartments.
STRING	A string of characters, that does not contains TAB, CR or LF
REAL	A real number
INTEGER	An integer number (possibly negative)
BOOLEAN	Either true or false