The MNXref namespace

MetaNetX/MNXref Release 4.4

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

1. The identifier of a chemical compound in an external resource [XREF]
2. The corresponding identifier in the MNXref namespace [MNX_ID]
3. 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

1. The identifier of the chemical compound in the MNXref namespace [MNX_ID]
2. The common name of the compound [STRING]
3. The reference compound, i.e. a compound selected in an external resource that best represent this entry [REFERENCE]
4. The formula of the compound [STRING]
5. The charge of the compound [INTEGER]
6. The mass of the compound [REAL]
7. The standard InChI of the compound [STRING]
8. The standard InChIKey of the compound [STRING]
9. The SMILES of the compound [STRING]

Nota Bene: The chemical data (e.g. formula, charge, mass, InChI, SMILES, InChIKey) are not necessarily the ones provided by the external resource for the selected reference: 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

1. The deprecated identifier [MNX_ID]
2. The replacement identifier [MNX_ID]
3. 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

chem_isom.tsv

1. The parent identifier [MNX_ID]
2. The child identifier [MNX_ID]
3. Relation description [STRING]

MNXref 4.2 release notes: - This is a new dataset - Describe the relation between parent and child identifiers with respect to stereochemistry, i.e. 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, but the overall graph is a acyclic

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 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

1. The deprecated identifier [MNX_ID]
2. The replacement identifier [MNX_ID]
3. 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

1. The identifier of a biochemical reaction in an external resource [XREF]
2. The corresponding identifier in the MNXref namespace [MNX_ID]
3. The biochemical reaction given by the external resource [STRING]

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]
3. The original best resource from where this reaction comes from [REFERENCE]
4. The EC(s) associated to this reaction [STRING]
5. Is the equation balanced with respect to elemental composition and charge [BOOLEAN]
6. 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

1. The deprecated identifier [MNX_ID]
2. The replacement identifier [MNX_ID]
3. 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

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 contain TAB, CR or LF

REAL

A real number

INTEGER

An integer number (possibly negative)

BOOLEAN

Either true or false