**MetaNetX / MNXref** *MNXref* | 1.0 & 1.1 | 2.0 | 3.0-> 3.2 | 4.0-> 4.2 | *Chemicals* | | | | | BioPath | 2010/05/03 | 2010/05/03 | | | BiGG | 2013/06/04 | 2015/09/02 | 2017/04/11 | 2019/10/31 | BKM/BRENDA | 2013/04/12 | | | | ChEBI | 102 | 131 | 150 | 185 | enviPath | | | 2017/04/12 | 2017/04/12 | HMDB | 3.0 | 3.6 | 3.6 | 4.0 | KEGG | 2013/04/12 | 75.1 | 82.0 | 93.0+ | LipidMaps | 2013/04/12 | 2015/06/28 | 2017/04/13 | 2019/10/02 | MetaCyc | 17.0 | 19.1 | 20.5 | 23.5 | Reactome | 2013/05/24 | 53 | 59 | 72 | SABIO-RK | | | 2016/05/27 | 2019/09/20 | SwissLipids | | | 2017/04/13 | 2020/03/19 | The SEED | 2013/04/12 | 2013/06/19 | 2017/04/13 | 2019/12/20 | UMBBD-EAWAG | | 2014/06/30 | | | UniPathway | 2012/04 | 2015/03 | | | *Reactions* | | | | | BioPath | 2010/05/03 | 2010/05/03 | | | BiGG | 2013/06/04 | 2015/09/02 | 2017/04/11 | 2019/10/31 | BKM/BRENDA | 2013/04/12 | | | | KEGG | 2013/04/12 | 75.1 | 82.0 | 93.0+ | MetaCyc | 17.0 | 19.1 | 20.5 | 23.5 | Reactome | 2013/05/24 | 53 | 59 | 72 | Rhea | 39 | 64 | 81 | 111 | SABIO-RK | | | 2016/05/27 | 2019/09/20 | The SEED | 2013/04/12 | 2013/06/19 | 2017/04/13 | 2019/12/20 | UniPathway | 2012/04 | 2015/03 | | | *Compartments* | | | | | BiGG | 2013/06/04 | 2015/09/02 | 2017/04/11 | 2019/10/31 | CCO | 17.0 | 19.1 | 20.5 | 23.5 | GO | 2012/06/09 | 2015/09/02 | 2017/04/11 | 2019/12/09 | The SEED | 2013/04/12 | 2013/06/19 | 2017/04/13 | 2019/12/20 | *Proteins* UniProt | 2013_06 | 2015_09 | 2017_04 | 2019_10 | *Version 4.2* - Add (secondary) prefixes compatible with identifiers.org, modification of some (primary) prefixes: Cross-references to identifiers.org were added when available. In previous MNXref releases the cross-references to identifiers.org were incomplete and were not using the "official" prefixes promoted by identifiers.org. When an entry can be referred by either a base IRI provided by the original resource or by a (secondary) IRI from identifiers.org, the former one is prefered. For example chebi:36927 corresponding to the original IRI is preferred over CHEBI:36927 with expanded form , despite these are the same resource and both "nomenclatures" are supported. Older identifiers.org paths starting like are not supported. As a matter of consequences some prefixes have been changed in the TSV files distribution of MNXref. In addition, in the RDF-turtle distribution, some IRI have been changed. Inconvenience regretted! - Repair computation of the major tautomer at pH 7.3. - Incorporate few mapping fixes. *Version 4.1* - Fix some protein complexes in GSMN/GEM. - Incorporate few mapping fixes. *Version 4.0* - Major improvement on structural definition and reconciliation. - Reconciliation improved to preserve reaction status in GSMN/GEM. - Some data source prefixes have changed to be synchronized with identifiers.org and our SPARQL endpoint. - Some columns have been reordered or suppressed, with respect to previous releases. - MNXM01 is now called PMF "Proton motive force". - OH(-) is referred to as MNXM02, distinct from H2O (WATER) now. - H3O(+) is referred to as MNXM03. - MNXR02 is the "passive" transport of protons. - MNXR03 is the "active" transport of protons, via PMF. *Version 3.2* - Fix duplicates in MetaNetX compounds. - Simplify reactions: no more float stoichiometric coefficients. - Exchange/boundary reactions are seen as other transport reactions. - Improve mapping of compounds with identical structures and different formula atom order. - Incorporate new mapping fixes. - Clean exclusion list for structure computation. *Version 3.1* - Incorporate new mapping fixes. - Better identification of complex/salt chemicals. - Merge most isotopes with their stable element. - Force split of BiGG chemicals appearing in the same reaction. - Add reaction original equation for most sources. - Fix for S atom stereochemistry. - Faster structural computations. *Version 3.0* - All reactions are compartmentalized now, using generic compartments. - Integrate SABIO-RK chemicals and reactions. - Integrate SwissLipids chemicals. - enviPath replaces UMBBD-EAWAG. - Do not use BioPath anymore, as our frozen data were too outdated. - Do not use UniPathway anymore, as most of its data are covered by Rhea and KEGG. - Use ChEBI ontology to help merge acids/bases and tautomers. - Add InChIKey for display, search and download. - Compute major tautomer at pH 7.3 from SMILES or InChI now if MOL files are not available. *Version 2.0* - Sum up in "MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks", Nucleic Acids Research (2016) 44(D1):D523-D526. (doi: 10.1093/nar/gkv1117) - Integrate UMBBD-EAWAG chemicals. - Do not use BKM/BRENDA as their public exported format is more ambiguous. - Full integration and use of MNXM01, as a transport proton. Add a MNXR01 reaction to transform MNXM01 to and from MNXM1 (balanced proton). - Use jChem/Marvin Beans version 6.2.0 for structural determination. We use the same version as Rhea to help data comparison. - Start to use an exception file for structural determination (from Rhea) to avoid some jChem/Marvin Beans issues with some structures. We extend this exception file with ChEBI & non-ChEBI identifiers. *Version 1.1* - Add MNXM01, used as a transport proton. - Harmonize Unicode and non-Unicode characters to help reconciliation: e.g. β -> beta - Remove fake InChI strings "unknown". - Remove extra "\", " |" or ";" strings in some compound names to help reconciliation. - Remove some invisible Unicode characters to help reconciliation. - Improve some cellular compartment mapping, mainly for CCO. - Fix MNXM114187 - ammonium hydroxide - formula. *Version 1.0* - Sum up in "Reconciliation of metabolites and biochemical reactions for metabolic networks", Brief Bioinform (2014) 15(1):123-135. (doi: 10.1093/bib/bbs058) - Use jChem/Marvin Beans version 5.10.3 for structural determination.