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metanetx_reactions — MetaNetX/MNXref reconciled metabolic reactions (2013-2025)

Description

Bipartite networks of metabolic reactions and metabolites from MNXref, the reconciled namespace of metabolites and biochemical reactions of MetaNetX (SIB Swiss Institute of Bioinformatics). MNXref merges the reactions and metabolites of the main metabolic databases and genome-scale models (e.g. BiGG, KEGG, MetaCyc, ModelSEED, Rhea, Reactome, SABIO-RK, ChEBI, HMDB, LipidMaps, SwissLipids), identifying the same metabolites and reactions across them, so that each reaction and each metabolite has a single MNXref identifier (MNXR..., MNXM...).

There is one network for each release of MNXref, from 1.0 (2013) to 4.5 (2025), named by its version: 1.0, 2.0, 3.0, 3.1, 3.2, 4.0, 4.1, 4.2, 4.3, 4.4 and 4.5. In each network, an edge goes from each metabolite of the left side of the equation of a reaction, as written by MNXref, to the reaction, and from the reaction to each metabolite of its right side, with the stoichiometric coefficient and, from version 3.0 on, the generic compartment of the metabolite (MNXD1 and MNXD2 for the two sides of a membrane in transport reactions, and in versions 3.x also MNXD3 to MNXD5, MNXDX and BOUNDARY). The direction of the reactions is not given by MNXref (the equations are written with =), so the direction of the edges is only that of the written equation. A metabolite that is transported between compartments appears on both sides of a reaction. Pseudo-metabolites of MNXref are kept as nodes, e.g. BIOMASS, WATER (the solvent, distinct from the water molecule MNXM2) and MNXM01 (a proton that is not balanced). Reactions without participants (e.g. EMPTY) are isolated nodes.

The networks have the following properties:

  • (Node) mnx_id: the MNXref identifier of the reaction (MNXR...) or of the metabolite (MNXM...).
  • (Node) is_reaction: whether the node is a reaction (otherwise it is a metabolite).
  • (Node) name: the name of the metabolite (empty for reactions, and for metabolites missing from the list of metabolites of the release).
  • (Node) reference: the source of the identifier, i.e. the first database in which it was found (e.g. bigg:10FTHF5GLUtl, chebi:15378).
  • (Node) ec: the EC numbers of the reaction, separated by ;.
  • (Node) balance: whether the reaction is balanced (in versions up to 3.2: true, false, ambiguous, NA or redox; from version 4.0: B for balanced, or empty).
  • (Node) is_transport (versions 4.x): whether the reaction is a transport reaction.
  • (Node) formula, charge, mass, inchikey: the formula, charge, mass and InChIKey of the metabolite (empty, 0 or NaN if not given; inchikey is not given in versions 1.0 and 2.0).
  • (Edge) coefficient: the stoichiometric coefficient of the metabolite, as given (e.g. 1, 2, 0.5, (n), (n+1)).
  • (Edge) compartment (versions from 3.0): the generic compartment of the metabolite in the reaction.
Tags
Biological Metabolic Chemical Unweighted Bipartite Metadata
Added
2026-10-31
Citation
  • S. Moretti, V. D. T. Tran, F. Mehl, M. Ibberson, M. Pagni, "MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models." Nucleic Acids Research 49, D570-D574 (2021) 10.1093/nar/gkaa992 Sci-Hub
  • S. Moretti, O. Martin, T. Van Du Tran, A. Bridge, A. Morgat, M. Pagni, "MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks." Nucleic Acids Research 44, D523-D526 (2016) 10.1093/nar/gkv1117 Sci-Hub
Upstream URL OK
https://www.metanetx.org/
https://www.metanetx.org/mnxdoc/mnxref.html
Upstream license
Creative Commons Attribution 4.0 International (CC BY 4.0); information from the external resources under their own licenses, https://www.metanetx.org/mnxdoc/mnxref.html
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
1.0 51,674 140,793 2.72 83.48 102.47 225.37 -0.14 0.00 28 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance formula charge mass coefficient 1.6 MiB 2.3 MiB 2.3 MiB 2.1 MiB
2.0 51,023 148,893 2.92 89.19 111.05 225.33 -0.14 0.00 28 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance formula charge mass coefficient 1.6 MiB 2.3 MiB 2.3 MiB 2.2 MiB
3.0 70,796 203,480 2.87 104.84 128.26 196.96 -0.14 0.00 26 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance formula charge mass inchikey coefficient compartment 2.4 MiB 3.5 MiB 3.4 MiB 3.2 MiB
3.1 72,266 208,246 2.88 106.24 129.64 196.96 -0.14 0.00 26 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance formula charge mass inchikey coefficient compartment 2.4 MiB 3.5 MiB 3.5 MiB 3.3 MiB
3.2 69,683 200,774 2.88 105.13 128.01 196.96 -0.14 0.00 26 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance formula charge mass inchikey coefficient compartment 2.4 MiB 3.4 MiB 3.4 MiB 3.2 MiB
4.0 116,326 335,320 2.88 109.07 140.35 216.14 -0.12 0.00 32 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance is_transport formula charge mass inchikey coefficient compartment 3.7 MiB 5.5 MiB 5.4 MiB 5.2 MiB
4.1 116,282 335,233 2.88 109.07 140.34 216.14 -0.12 0.00 32 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance is_transport formula charge mass inchikey coefficient compartment 3.8 MiB 5.6 MiB 5.6 MiB 5.2 MiB
4.2 116,068 334,980 2.89 109.32 140.26 215.95 -0.12 0.00 32 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance is_transport formula charge mass inchikey coefficient compartment 3.7 MiB 5.5 MiB 5.5 MiB 5.2 MiB
4.3 117,308 336,913 2.87 110.04 140.81 293.13 -0.12 0.00 32 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance is_transport formula charge mass inchikey coefficient compartment 3.7 MiB 5.5 MiB 5.5 MiB 5.3 MiB
4.4 117,167 336,567 2.87 109.98 140.72 293.14 -0.12 0.00 32 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance is_transport formula charge mass inchikey coefficient compartment 3.7 MiB 5.6 MiB 5.5 MiB 5.3 MiB
4.5 131,442 382,400 2.91 121.66 153.79 293.10 -0.13 0.00 32 0.99 Directed Bipartite mnx_id is_reaction name reference ec balance is_transport formula charge mass inchikey coefficient compartment 4.2 MiB 6.3 MiB 6.2 MiB 5.9 MiB