Search MNXref
SystemsX.ch
The Swiss Initiative in Systems Biology

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

CC by 4.0 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 3.0 data sources
Data source nameData source version
Chemicals
BiGG2017/04/11
ChEBI 150
enviPath 2017/04/12
HMDB 3.6
KEGG 82.0
LipidMaps 2017/04/13
MetaCyc 20.5
Reactome 59
SABIO-RK 2016/05/27
SwissLipids 2017/04/13
The SEED 2017/04/13
Reactions
BiGG2017/04/11
KEGG 82.0
MetaCyc 20.5
Reactome 59
Rhea 81
SABIO-RK 2016/05/27
The SEED 2017/04/13
Compartments
BiGG 2017/04/11
CCO20.5
GO 2017/04/11
The SEED 2017/04/13
Proteins
UniProt2017_04

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.
File nameColumn content
chem_xref.tsv
  1. The identifier of a chemical compound in an external resource [XREF]
  2. The corresponding identifier in the MNXref namespace [MNX_ID]
  3. The evidence tag for the mapping: identity for identical structures; structural when the major tautomers at pH 7.3 have identical structures; inferred when deduced through the reactions or cross-references [STRING]
  4. The description given by the external resource [STRING]
chem_prop.tsv
  1. The identifier of the chemical compound in the MNXref namespace [MNX_ID]
  2. The common name of the compound [STRING]
  3. The formula of the compound [STRING]
  4. The charge of the compound [INTEGER]
  5. The mass of the compound [REAL]
  6. The standard InChI of the compound [STRING]
  7. The SMILES of the compound [STRING]
  8. The original resource from where this compound comes from [XREF]
  9. The standard InChIKey of the compound [STRING]    Added in MNXref 3.0
comp_xref.tsv
  1. The identifier of a sub-cellular compartment in an external resource [XREF]
  2. The corresponding identifier in the MNXref namespace [MNX_ID]
  3. The description given by the external resource [STRING]
comp_prop.tsv
  1. The identifier of the sub-cellular compartment in the namespace [MNX_ID]
  2. The common name of that compartment [STRING]
  3. The original resource from where this compartment comes from [XREF]
reac_xref.tsv
  1. The identifier of a biochemical reaction in an external resource [XREF]
  2. The corresponding identifier in the MNXref namespace [MNX_ID]
reac_prop.tsv
  1. The identifier of the reaction in the MNXref namespace [MNX_ID]
  2. Equation of the reaction in the MNXref namespace (compartmentalized and undirected) [EQUA]    New format in MNXref version 3.0!
  3. Equation of the reaction in human readable form [STRING]
  4. Is the equation balanced with respect to elemental composition and charge [BOOLEAN]
  5. The EC(s) associated to this reaction [STRING]
  6. The original resource from where this reaction comes from [XREF]

Data types
TypeSpecification
MNX_IDA 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
XREFAn 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 identifers 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.
STRINGA string of characters, that does not contains TAB, CR or LF
REALA real number
INTEGERAn integer number (possibly negative)
BOOLEANEither true or false