MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions, providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models Sébastien Moretti, Van Du T Tran, Florence Mehl, Mark Ibberson, Marco Pagni Nucleic Acids Research (2021), 49(D1):D570-D574 2017-11-13 MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models 2017-12-01 2024-05-14 MetaNetX Ontology mnx GSMN reconstruction is one of the foundations of Systems Biology. The development of such reconstruction involves the integration of knowledge about reactions and metabolites from the scientific literature, public databases and previously published GSMNs. Historically, many GSMNs were formulated using metabolites represented as "symbols", i.e. without explicit reference to a molecular structure. The initial motivation for creating this resource ten years ago was to add molecular structures to existing GSMNs. More generally, the goal was to establish cross-links between symbols in GSMNs published by different groups and the molecules found in the major biochemical databases. This problem is trivial as long as one-to-one mappings can be established between the different resources, but this is not always the case. Merging metabolites in a metabolic network may lead to the merging of reactions, possibly altering the model properties, and hence the predictions that could be made using it. <br> <img src="https://www.metanetx.org/images/MNXref_schema.png" alt="drawing" width="800"/> contains the following catalyzers (enzymatic complex(s) and flux constraints) A predicate to design the public IRI that best represents a MNXref metabolite indicate how to replace a deprecated entity A predicate to design the public IRI that best represents a MNXref metabolite A predicate to list all public IRIs that are included in a MNXref metabolite A predicate to design the public IRI that best represents a MNXref compartment indicate how to replace a deprecated entity A predicate to design the public IRI that best represents a MNXref compartment A predicate to list all public IRIs that are included in a MNXref compartment requires the full list of genes or proteins to be functional A predicate to list all gene name that correspond to a gene or a protein A predicate to list GPRs that make the core of any model A predicate to specify the parts (mnx:PART) on the left side of a chemical equation (mnx:REAC) belongs to the MNXref reaction implies the list of genes or proteins (no logical constraint specified here) A predicate to list all public IRIs that correspond to a gene or a protein contains the following catalyzers (mnx:CATA) A predicate to design the public IRI that best represents a MNXref reaction indicate how to replace a deprecated entity A predicate to design the public IRI that best represents a MNXref reaction A predicate to list all public IRIs that are included in a MNXref reaction A predicate to specify the parts (mnx:PART) on the right side of a chemical equation (mnx:REAC) A predicate to specify the parts (mnx:PART) on the both sides of a chemical equation (mnx:REAC) A predicate to enumerate sub-units (mnx:PEPT) that make of an enzyme or transporter (mnx:CPLX) is the model able to simulate growth Number of chemicals identifies metabolites in MNXref Number of compartments identifies (generic) compartments in MNXref Is the reaction balanced? tags generic/placeholder compartment Organism lineage Organism name Number of genes/peptides Cites a PubMed identifier Number of reactions identifies reactions in MNXref Number of compartmentalized chemical species indicates an NCBI Taxid The type of a helper class to describe one or several protein complexes The type of all metabolites The type of all sub-cellular compartments, including specific and generic compartments A symbol for reaction which both sides are empty, and that should not appear in a model. Typically, acid-base reactions become empty as the reconciliation merges different protonation states of a given metabolite. mnx:EMPTY The type for Gene-Protein-Reaction, i.e. this is a helper class to associate a reaction (mnx:REAC) with zero, one or more catalyzers (mnx:CATA) An artificial reaction that exchange proton for PMF (a very trumpian deal) mnx:MNXR01 The type for a helper class, consisting of a compartmentalized chemical species (mnx:CHEM and mnx:COMP) associated with a particular stoichiometric coefficient The type for a gene or a protein that appears in MetaNetX models The type of all reactions, as defined in MNXref (with generic compartments) and in MetaNetX models (with specific compartments) Marco Pagni Marco Pagni Sébastien Moretti Sébastien Moretti A symbol to represent biomass mnx:BIOMASS A symbol to represent a model boundary and that appears in so-called external reactions mnx:BOUNDARY A symbol to represent hydroxide (OH-). In principle, it can be substituted for mnx:PROTON or mnx:PMF on the other side of a chemical equation, hence it should not appear in MetaNetX models mnx:HYDROXYDE A symbol to represent the proton motive force (PMF). PMF is often confounded with (balance) proton. MetaNetX attempts to distinguish them systematically mnx:PMF A symbol to represent the proton (H+) that is used to balance chemical equations mnx:PROTON A symbol to tag reactions that occur spontaneously mnx:SPONTANEOUS A symbol to represent water mnx:WATER The object molecule has a more detailed description of its stereochemistry (either enantiomers or cis-trans isomers) than the subject molecule, i.e. the subject molecule encompasses the object molecule true The object reaction has a more detailed description of the stereochemistry of its reactants than the subject reaction