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.
DisclaimerExcept 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.
|Data source name||Data source version|
|Previous releases of the MNXref namespace are available at MNXref FTP.|
|All data files are made of TAB-delimited values. Comment lines starting with # appear at the beginning of all files.|
|File name||Column content|
|MNX_ID||A 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|
|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|
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.
|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|