@prefix : . @prefix owl: . @prefix rdf: . @prefix xml: . @prefix xsd: . @prefix rdfs: . @base . rdf:type owl:Ontology ; owl:versionIRI ; "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"^^xsd:date ; , ; """ MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models""" ; "2017-12-01"^^xsd:date ; ; "2024-05-14"^^xsd:date ; "MetaNetX Ontology"@en ; "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.
\"drawing\" """ . ################################################################# # Annotation properties ################################################################# ### http://purl.org/dc/terms/abstract rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/bibliographicCitation rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/created rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/creator rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/description rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/issue rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/license rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/modified rdf:type owl:AnnotationProperty . ### http://purl.org/dc/terms/title rdf:type owl:AnnotationProperty . ### http://purl.org/vocab/vann/preferredNamespacePrefix rdf:type owl:AnnotationProperty . ### http://purl.org/vocab/vann/preferredNamespaceUri rdf:type owl:AnnotationProperty . ### https://rdf.metanetx.org/schema/hasIsomericChild :hasIsomericChild rdf:type owl:AnnotationProperty . ### https://rdf.metanetx.org/schema/reacIsom :reacIsom rdf:type owl:AnnotationProperty ; rdfs:subPropertyOf :hasIsomericChild . ### https://schema.org/affiliation rdf:type owl:AnnotationProperty . ### https://schema.org/email rdf:type owl:AnnotationProperty . ### https://schema.org/name rdf:type owl:AnnotationProperty . ### https://w3id.org/widoco/vocab#introduction rdf:type owl:AnnotationProperty . ################################################################# # Datatypes ################################################################# ### http://www.w3.org/2001/XMLSchema#date xsd:date rdf:type rdfs:Datatype . ################################################################# # Object Properties ################################################################# ### https://rdf.metanetx.org/schema/cata :cata rdf:type owl:ObjectProperty ; rdfs:domain :GPR ; rdfs:range :CATA ; rdfs:comment "contains the following catalyzers (enzymatic complex(s) and flux constraints)" . ### https://rdf.metanetx.org/schema/chemIsom :chemIsom rdf:type owl:ObjectProperty ; rdfs:domain :CHEM ; rdfs:range :CHEM . ### https://rdf.metanetx.org/schema/chemRefer :chemRefer rdf:type owl:ObjectProperty ; rdfs:domain :CHEM ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to design the public IRI that best represents a MNXref metabolite" . ### https://rdf.metanetx.org/schema/chemReplacedBy :chemReplacedBy rdf:type owl:ObjectProperty ; rdfs:domain :CHEM ; rdfs:range :CHEM ; rdfs:comment "indicate how to replace a deprecated entity" . ### https://rdf.metanetx.org/schema/chemSource :chemSource rdf:type owl:ObjectProperty ; rdfs:domain :CHEM ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to design the public IRI that best represents a MNXref metabolite" . ### https://rdf.metanetx.org/schema/chemXref :chemXref rdf:type owl:ObjectProperty ; rdfs:domain :CHEM ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to list all public IRIs that are included in a MNXref metabolite" . ### https://rdf.metanetx.org/schema/compRefer :compRefer rdf:type owl:ObjectProperty ; rdfs:domain :COMP ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to design the public IRI that best represents a MNXref compartment" . ### https://rdf.metanetx.org/schema/compReplacedBy :compReplacedBy rdf:type owl:ObjectProperty ; rdfs:domain :COMP ; rdfs:range :COMP ; rdfs:comment "indicate how to replace a deprecated entity" . ### https://rdf.metanetx.org/schema/compSource :compSource rdf:type owl:ObjectProperty ; rdfs:domain :COMP ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to design the public IRI that best represents a MNXref compartment" . ### https://rdf.metanetx.org/schema/compXref :compXref rdf:type owl:ObjectProperty ; rdfs:domain :COMP ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to list all public IRIs that are included in a MNXref compartment" . ### https://rdf.metanetx.org/schema/cplx :cplx rdf:type owl:ObjectProperty ; rdfs:domain :CATA ; rdfs:range :CPLX ; rdfs:comment "requires the full list of genes or proteins to be functional" . ### https://rdf.metanetx.org/schema/geneName :geneName rdf:type owl:ObjectProperty ; rdfs:domain :PEPT ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to list all gene name that correspond to a gene or a protein" . ### https://rdf.metanetx.org/schema/gpr :gpr rdf:type owl:ObjectProperty ; rdfs:domain :MNET ; rdfs:range :GPR ; rdfs:comment "A predicate to list GPRs that make the core of any model" . ### https://rdf.metanetx.org/schema/left :left rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range :PART ; rdfs:comment "A predicate to specify the parts (mnx:PART) on the left side of a chemical equation (mnx:REAC)" . ### https://rdf.metanetx.org/schema/mnxr :mnxr rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range :REAC ; rdfs:comment "belongs to the MNXref reaction" . ### https://rdf.metanetx.org/schema/pept :pept rdf:type owl:ObjectProperty ; rdfs:domain :CATA ; rdfs:range :PEPT ; rdfs:comment "implies the list of genes or proteins (no logical constraint specified here)" . ### https://rdf.metanetx.org/schema/peptXref :peptXref rdf:type owl:ObjectProperty ; rdfs:domain :PEPT ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to list all public IRIs that correspond to a gene or a protein" . ### https://rdf.metanetx.org/schema/reac :reac rdf:type owl:ObjectProperty ; rdfs:domain :GPR ; rdfs:range :REAC ; rdfs:comment "contains the following catalyzers (mnx:CATA)" . ### https://rdf.metanetx.org/schema/reacIsom :reacIsom rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range :REAC . ### https://rdf.metanetx.org/schema/reacRefer :reacRefer rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to design the public IRI that best represents a MNXref reaction" . ### https://rdf.metanetx.org/schema/reacReplacedBy :reacReplacedBy rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range :REAC ; rdfs:comment "indicate how to replace a deprecated entity" . ### https://rdf.metanetx.org/schema/reacSource :reacSource rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to design the public IRI that best represents a MNXref reaction" . ### https://rdf.metanetx.org/schema/reacXref :reacXref rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range rdfs:Resource ; rdfs:comment "A predicate to list all public IRIs that are included in a MNXref reaction" . ### https://rdf.metanetx.org/schema/right :right rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range :PART ; rdfs:comment "A predicate to specify the parts (mnx:PART) on the right side of a chemical equation (mnx:REAC)" . ### https://rdf.metanetx.org/schema/side :side rdf:type owl:ObjectProperty ; rdfs:domain :REAC ; rdfs:range :PART ; rdfs:comment "A predicate to specify the parts (mnx:PART) on the both sides of a chemical equation (mnx:REAC)" ; rdfs:seeAlso . ### https://rdf.metanetx.org/schema/subu :subu rdf:type owl:ObjectProperty ; rdfs:domain :CPLX ; rdfs:range :PEPT ; rdfs:comment "A predicate to enumerate sub-units (mnx:PEPT) that make of an enzyme or transporter (mnx:CPLX)" . ################################################################# # Data properties ################################################################# ### https://rdf.metanetx.org/schema/canGrow :canGrow rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:string ; rdfs:comment "is the model able to simulate growth" . ### https://rdf.metanetx.org/schema/charge :charge rdf:type owl:DatatypeProperty ; rdfs:domain :CHEM ; rdfs:range xsd:integer ; rdfs:comment "" . ### https://rdf.metanetx.org/schema/chemCount :chemCount rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:integer ; rdfs:comment "Number of chemicals" . ### https://rdf.metanetx.org/schema/chemInMNXref :chemInMNXref rdf:type owl:DatatypeProperty ; rdfs:domain :CHEM ; rdfs:range xsd:boolean ; rdfs:comment "identifies metabolites in MNXref" . ### https://rdf.metanetx.org/schema/classification :classification rdf:type owl:DatatypeProperty ; rdfs:domain :REAC ; rdfs:range xsd:string . ### https://rdf.metanetx.org/schema/compCount :compCount rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:integer ; rdfs:comment "Number of compartments" . ### https://rdf.metanetx.org/schema/compInMNXref :compInMNXref rdf:type owl:DatatypeProperty ; rdfs:domain :COMP ; rdfs:range xsd:boolean ; rdfs:comment "identifies (generic) compartments in MNXref" . ### https://rdf.metanetx.org/schema/formula :formula rdf:type owl:DatatypeProperty ; rdfs:domain :CHEM ; rdfs:range xsd:string ; rdfs:comment "" . ### https://rdf.metanetx.org/schema/inchi :inchi rdf:type owl:DatatypeProperty ; rdfs:domain :CHEM ; rdfs:range xsd:string ; rdfs:comment "" . ### https://rdf.metanetx.org/schema/inchikey :inchikey rdf:type owl:DatatypeProperty ; rdfs:domain :CHEM ; rdfs:range xsd:string ; rdfs:comment "" . ### https://rdf.metanetx.org/schema/isBalanced :isBalanced rdf:type owl:DatatypeProperty ; rdfs:domain :REAC ; rdfs:range xsd:boolean ; rdfs:comment "Is the reaction balanced?" . ### https://rdf.metanetx.org/schema/isGenericComp :isGenericComp rdf:type owl:DatatypeProperty ; rdfs:domain :COMP ; rdfs:range xsd:boolean ; rdfs:comment "tags generic/placeholder compartment" . ### https://rdf.metanetx.org/schema/isTransport :isTransport rdf:type owl:DatatypeProperty ; rdfs:domain :REAC ; rdfs:range xsd:boolean . ### https://rdf.metanetx.org/schema/lineage :lineage rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:string ; rdfs:comment "Organism lineage" . ### https://rdf.metanetx.org/schema/mass :mass rdf:type owl:DatatypeProperty ; rdfs:domain :CHEM ; rdfs:range xsd:decimal ; rdfs:comment "" . ### https://rdf.metanetx.org/schema/organism :organism rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:string ; rdfs:comment "Organism name" . ### https://rdf.metanetx.org/schema/peptCount :peptCount rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:integer ; rdfs:comment "Number of genes/peptides" . ### https://rdf.metanetx.org/schema/pmid :pmid rdf:type owl:DatatypeProperty ; rdfs:range :MNET ; rdfs:comment "Cites a PubMed identifier" . ### https://rdf.metanetx.org/schema/reacCount :reacCount rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:integer ; rdfs:comment "Number of reactions" . ### https://rdf.metanetx.org/schema/reacInMNXref :reacInMNXref rdf:type owl:DatatypeProperty ; rdfs:domain :REAC ; rdfs:range xsd:boolean ; rdfs:comment "identifies reactions in MNXref" . ### https://rdf.metanetx.org/schema/smiles :smiles rdf:type owl:DatatypeProperty ; rdfs:domain :CHEM ; rdfs:range xsd:string ; rdfs:comment "" . ### https://rdf.metanetx.org/schema/specCount :specCount rdf:type owl:DatatypeProperty ; rdfs:domain :MNET ; rdfs:range xsd:integer ; rdfs:comment "Number of compartmentalized chemical species" . ### https://rdf.metanetx.org/schema/taxid :taxid rdf:type owl:DatatypeProperty ; rdfs:range :MNET ; rdfs:comment "indicates an NCBI Taxid" . ################################################################# # Classes ################################################################# ### http://www.w3.org/2000/01/rdf-schema#Resource rdfs:Resource rdf:type owl:Class . ### http://www.w3.org/ns/prov#Person rdf:type owl:Class . ### http://xmlns.com/foaf/0.1/Person rdf:type owl:Class . ### https://rdf.metanetx.org/schema/CATA :CATA rdf:type owl:Class ; rdfs:comment "The type of a helper class to describe one or several protein complexes" . ### https://rdf.metanetx.org/schema/CHEM :CHEM rdf:type owl:Class ; rdfs:comment "The type of all metabolites" . ### https://rdf.metanetx.org/schema/COMP :COMP rdf:type owl:Class ; rdfs:comment "The type of all sub-cellular compartments, including specific and generic compartments" . ### https://rdf.metanetx.org/schema/CPLX :CPLX rdf:type owl:Class . ### https://rdf.metanetx.org/schema/EMPTY :EMPTY rdf:type owl:Class ; rdfs:comment "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." ; rdfs:label "mnx:EMPTY " . ### https://rdf.metanetx.org/schema/GPR :GPR rdf:type owl:Class ; rdfs:comment "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)" . ### https://rdf.metanetx.org/schema/MNXR01 :MNXR01 rdf:type owl:Class ; rdfs:comment "An artificial reaction that exchange proton for PMF (a very trumpian deal)" ; rdfs:label "mnx:MNXR01" . ### https://rdf.metanetx.org/schema/PART :PART rdf:type owl:Class ; rdfs:comment "The type for a helper class, consisting of a compartmentalized chemical species (mnx:CHEM and mnx:COMP) associated with a particular stoichiometric coefficient" . ### https://rdf.metanetx.org/schema/PEPT :PEPT rdf:type owl:Class ; rdfs:comment "The type for a gene or a protein that appears in MetaNetX models" . ### https://rdf.metanetx.org/schema/REAC :REAC rdf:type owl:Class ; rdfs:comment "The type of all reactions, as defined in MNXref (with generic compartments) and in MetaNetX models (with specific compartments)" . ################################################################# # Individuals ################################################################# ### https://orcid.org/0000-0001-9292-9463 rdf:type owl:NamedIndividual , , ; rdfs:label "Marco Pagni" ; ; ; "Marco Pagni" . ### https://orcid.org/0000-0003-3947-488X rdf:type owl:NamedIndividual , , ; rdfs:label "Sébastien Moretti" ; ; ; "Sébastien Moretti" . ### https://rdf.metanetx.org/schema/BIOMASS :BIOMASS rdf:type owl:NamedIndividual , :CHEM ; rdfs:comment "A symbol to represent biomass" ; rdfs:label "mnx:BIOMASS" . ### https://rdf.metanetx.org/schema/BOUNDARY :BOUNDARY rdf:type owl:NamedIndividual , :COMP ; rdfs:comment "A symbol to represent a model boundary and that appears in so-called external reactions" ; rdfs:label "mnx:BOUNDARY" . ### https://rdf.metanetx.org/schema/HYDROXYDE :HYDROXYDE rdf:type owl:NamedIndividual , :CHEM ; rdfs:comment "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" ; rdfs:label "mnx:HYDROXYDE" . ### https://rdf.metanetx.org/schema/PMF :PMF rdf:type owl:NamedIndividual , :CHEM ; rdfs:comment "A symbol to represent the proton motive force (PMF). PMF is often confounded with (balance) proton. MetaNetX attempts to distinguish them systematically" ; rdfs:label "mnx:PMF" . ### https://rdf.metanetx.org/schema/PROTON :PROTON rdf:type owl:NamedIndividual , :CHEM ; rdfs:comment "A symbol to represent the proton (H+) that is used to balance chemical equations" ; rdfs:label "mnx:PROTON" . ### https://rdf.metanetx.org/schema/SPONTANEOUS :SPONTANEOUS rdf:type owl:NamedIndividual , :PEPT ; rdfs:comment "A symbol to tag reactions that occur spontaneously" ; rdfs:label "mnx:SPONTANEOUS" . ### https://rdf.metanetx.org/schema/WATER :WATER rdf:type owl:NamedIndividual , :CHEM ; rdfs:comment "A symbol to represent water" ; rdfs:label "mnx:WATER" . ### https://rdf.metanetx.org/schema/chemIsom :chemIsom rdf:type owl:NamedIndividual ; owl:sameAs :hasIsomericChild . ### https://rdf.metanetx.org/schema/hasIsomericChild :hasIsomericChild rdf:type owl:NamedIndividual . ### https://rdf.metanetx.org/schema/hasIsomericChild :hasIsomericChild rdf:type owl:NamedIndividual . ################################################################# # Annotations ################################################################# :chemIsom rdfs:comment "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" . :hasIsomericChild owl:deprecated "true"^^xsd:boolean . :reacIsom rdfs:comment "The object reaction has a more detailed description of the stereochemistry of its reactants than the subject reaction" . ### Generated by the OWL API (version 5.1.18) https://github.com/owlcs/owlapi/