## MetaNetX/MNXref Release 4.2 The method to compute the MNXref namespace was first 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. Since, the algorithm has been improving. 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. ###[chem_xref.tsv](/cgi-bin/mnxget/mnxref/chem_xref.tsv) 1. The identifier of a chemical compound in an external resource [[XREF](#XREF)] 2. The corresponding identifier in the MNXref namespace [[MNX_ID](#MNX_ID)] 3. The description given by the external resource [[STRING](#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](/cgi-bin/mnxget/mnxref/chem_prop.tsv) 1. The identifier of the chemical compound in the MNXref namespace [[MNX_ID](#MNX_ID)] 2. The common name of the compound [[STRING](#STRING)] 3. The original best resource from where this compound comes from [[REFERENCE](#REFERENCE)] 4. The formula of the compound [[STRING](#STRING)] 5. The charge of the compound [[INTEGER](#INTEGER)] 6. The mass of the compound [[REAL](#REAL)] 7. The standard InChI of the compound [[STRING](#STRING)] 8. The standard InChIKey of the compound [[STRING](#STRING)] 9. The SMILES of the compound [[STRING](#STRING)] Nota Bene: The chemical data (e.g. formula, charge, mass, InChI, SMILES, InChIKey) are not necessarily the ones provided by the selected source: Isotope information is removed; The protonation state might differ; R-group(s) may have been renamed.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](/cgi-bin/mnxget/mnxref/chem_depr.tsv) 1. The deprecated identifier [[MNX_ID](#MNX_ID)] 2. The replacement identifier [[MNX_ID](#MNX_ID)] 3. This happened in this MNXref version [[STRING](#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
###[chem_isom.tsv](/cgi-bin/mnxget/mnxref/chem_isom.tsv) 1. The parent identifier [[MNX_ID](#MNX_ID)] 2. The child identifier [[MNX_ID](#MNX_ID)] 3. Relation description [[STRING](#STRING)]MNXref 4.2 release notes: - This is a new dataset - Describe the relation between parent and child identifiers with respect to stereochemistry, the parent molecule includes the child molecule. For example alanine is a parent of L-alanine - One-to-one, many-to-one and one-to-many relations are possible
###[comp_xref.tsv](/cgi-bin/mnxget/mnxref/comp_xref.tsv) 1. The identifier of a sub-cellular compartment in an external resource [[XREF](#XREF)] 2. The corresponding identifier in the MNXref namespace [[MNX_ID](#MNX_ID)] 3. The description given by the external resource [[STRING](#STRING)] ###[comp_prop.tsv](/cgi-bin/mnxget/mnxref/comp_prop.tsv) 1. The identifier of the sub-cellular compartment in the namespace [[MNX_ID](#MNX_ID)] 2. The common name of that compartment [[STRING](#STRING)] 3. The original best resource from where this compartment comes from [[REFERENCE](#REFERENCE)]MNXref 4.0 release notes: - The content of this file was drastically simplified/sanitized
###[comp_depr.tsv](/cgi-bin/mnxget/mnxref/comp_depr.tsv) 1. The deprecated identifier [[MNX_ID](#MNX_ID)] 2. The replacement identifier [[MNX_ID](#MNX_ID)] 3. This happened in this MNXref version [[STRING](#STRING)]MNXref 4.0 release notes: - This is currently an empty dataset (placeholder) that will be filled in future release
###[reac_xref.tsv](/cgi-bin/mnxget/mnxref/reac_xref.tsv) 1. The identifier of a biochemical reaction in an external resource [[XREF](#XREF)] 2. The corresponding identifier in the MNXref namespace [[MNX_ID](#MNX_ID)] 3. The biochemical reaction given by the external resource [[STRING](#STRING)] ###[reac_prop.tsv](/cgi-bin/mnxget/mnxref/reac_prop.tsv) 1. The identifier of the reaction in the MNXref namespace [[MNX_ID](#MNX_ID)] 2. Equation of the reaction in the MNXref namespace (compartmentalized and undirected) [[EQUA](#EQUA)] 3. The original best resource from where this reaction comes from [[REFERENCE](#REFERENCE)] 4. The EC(s) associated to this reaction [[STRING](#STRING)] 5. Is the equation balanced with respect to elemental composition and charge [[BOOLEAN](#BOOLEAN)] 6. Is this a transport reaction [[BOOLEAN](#BOOLEAN)]MNXref 4.0 release notes: - !!! The columns were reordered !!! - The column *human readable equation* was suppressed
###[reac_depr.tsv](/cgi-bin/mnxget/mnxref/reac_depr.tsv) 1. The deprecated identifier [[MNX_ID](#MNX_ID)] 2. The replacement identifier [[MNX_ID](#MNX_ID)] 3. This happened in this MNXref version [[STRING](#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
## MetaNetX special identifiers A few identifiers are defined by MetaNetX/MNXref, as they deserve particular treatment while manipulating metabolic networks. ### Special identifiers for compounds **BIOMASS** is used to explicitly tag growth-related equations. **MNXM1** is used to represent H(+) that are freely used to balance chemical equations in aqueous solution. It was designated by MNXM1 in MetaNetX/MNXref releases prior to 4.0. **MNXM01** is used to represent the Proton Motive Force (PMF), often represented as transported H(+) in published GSMN. It was designated by MNXM01 in MetaNetX/MNXref releases prior to 4.0. **WATER** was designated by MNXM2 in MetaNetX/MNXref releases prior to 4.0. **MNXM02** is used to represent OH(-) in MetaNetX/MNXref. While processing models, it is systematically replaced by H2O - H(+), the latter proton being interpreted as MXNM1 or MNXM01 depending on the reaction context. This symbol was missing in MetaNetX/MNXref releases prior to 4.0. ### Special identifiers for reactions **EMPTY** represents an equation with empty terms on both the left and the right sides. These arise after mapping the chemical species onto MetaNetX/MNXref and simplifying them. Acid-base and/or tautomer reactions belong to this class. ### Special identifiers for compartments **BOUNDARY** is used to tag *external* exchange reactions. As a consequence, reaction with an empty side are forbidden here. ### Special symbols for peptides/genes **SPONTANEOUS** is used to tag *spontaneous* reactions. Reactions with no enzymes nor this tag have an unknown or unspecified catalyst. ## Data types ### 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. _MNXR190823_ ### 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`