@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 Schema Vocabulary: defines all classes and properties for metabolites, reactions, compartments, and metabolic network models in the MetaNetX/MNXref reconciliation framework." ;
"2017-12-01"^^xsd:date ;
;
"2024-05-14"^^xsd:date ;
"MetaNetX Schema Vocabulary"@en ;
"mnx" ;
;
rdfs:comment """The MetaNetX Schema defines all classes and properties used to describe
metabolites, reactions, compartments, and metabolic network models in the MetaNetX/MNXref
reconciliation framework. All terms in this vocabulary use the 'mnx:' prefix and are
explicitly linked to this ontology via rdfs:isDefinedBy."""@en ;
rdfs:label "MetaNetX Schema Vocabulary"@en ;
"""
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\"](\"https://www.metanetx.org/images/MNXref_schema.png\")
""" .
#################################################################
# 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 .
### http://www.w3.org/1999/02/22-rdf-syntax-ns#comment
rdf:comment rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#closeMatch
rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#example
rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#inScheme
rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#note
rdf:type owl:AnnotationProperty .
### https://rdf.metanetx.org/schema/default_LB
:default_LB rdfs:comment "Default lower bound for flux constraints" ;
rdfs:isDefinedBy ;
rdf:type owl:AnnotationProperty ;
rdfs:domain :MNET .
### https://rdf.metanetx.org/schema/default_UB
:default_UB rdfs:comment "Default upper bound for flux constraints" ;
rdfs:isDefinedBy ;
rdf:type owl:AnnotationProperty ;
rdfs:domain :MNET .
### https://rdf.metanetx.org/schema/dir
:dir rdfs:comment "Direction of reaction" ;
rdfs:isDefinedBy ;
rdf:type owl:AnnotationProperty ;
rdfs:domain :CATA .
### https://rdf.metanetx.org/schema/hasIsomericChild
:hasIsomericChild rdf:type owl:AnnotationProperty .
### https://rdf.metanetx.org/schema/lb
:lb rdfs:comment "Lower bound for flux constraint" ;
rdfs:isDefinedBy ;
rdf:type owl:AnnotationProperty ;
rdfs:domain :CATA .
### https://rdf.metanetx.org/schema/reacIsom
:reacIsom rdf:type owl:AnnotationProperty ;
rdfs:subPropertyOf :hasIsomericChild .
### https://rdf.metanetx.org/schema/ub
:ub rdfs:comment "Upper bound for flux constraint" ;
rdfs:isDefinedBy ;
rdf:type owl:AnnotationProperty ;
rdfs:domain :CATA .
### 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)" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/chemXref
:chemXref rdf:type owl:ObjectProperty ;
rdfs:domain :CHEM ;
rdfs:range rdfs:Resource .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/elemFormula
:elemFormula rdf:type owl:ObjectProperty ;
rdfs:domain :ChemXRef ;
rdfs:range :ElemFormula ;
rdfs:comment "Atomic composition of a pure compounds is made of several instances of mnx:ElemFormula" ;
rdfs:isDefinedBy ;
rdfs:label "has elemental composition" .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/isClassifiedUnder
:isClassifiedUnder rdf:type owl:ObjectProperty ;
rdfs:domain :MolCategory ;
rdfs:range :chemXref ;
rdfs:comment "The chemical entity is classified under one, or several molecular categories." ;
rdfs:isDefinedBy ;
rdfs:label "is classified under" .
### 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)" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/mnxr
:mnxr rdf:type owl:ObjectProperty ;
rdfs:domain :REAC ;
rdfs:range :REAC ;
rdfs:comment "belongs to the MNXref reaction" ;
rdfs:isDefinedBy .
### 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)" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/peptRefer
:peptRefer rdf:type owl:ObjectProperty ;
rdfs:domain :PEPT ;
rdfs:range rdfs:Resource ;
rdfs:comment "Reference for peptide/gene" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/peptSource
:peptSource rdf:type owl:ObjectProperty ;
rdfs:domain :PEPT ;
rdfs:range rdfs:Resource ;
rdfs:comment "Source of peptide/gene information" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/pmid
:pmid rdf:type owl:ObjectProperty ;
rdfs:range :MNET ;
rdfs:comment "Cites a PubMed identifier" ;
rdfs:isDefinedBy .
### 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)" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy ;
rdfs:label "has reference chem" .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### 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)" ;
rdfs:isDefinedBy .
### 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:isDefinedBy ;
rdfs:seeAlso .
### https://rdf.metanetx.org/schema/structIsReplacedBy
:structIsReplacedBy rdf:type owl:ObjectProperty ;
rdfs:domain :ChemXRef ;
rdfs:range :ChemXRef .
### https://rdf.metanetx.org/schema/structureDerivedFrom
:structureDerivedFrom rdf:type owl:ObjectProperty ;
rdfs:domain :ChemXRef ;
rdfs:range :ChemXRef .
### 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)" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/taxid
:taxid rdf:type owl:ObjectProperty ;
rdfs:range :MNET ;
rdfs:comment "indicates an NCBI Taxid" ;
rdfs:isDefinedBy .
#################################################################
# Data properties
#################################################################
### https://rdf.metanetx.org/schema/atomCount
:atomCount rdf:type owl:DatatypeProperty ;
rdfs:domain :ElemFormula ;
rdfs:range xsd:double ;
rdfs:comment "A positive number" ;
rdfs:isDefinedBy ;
rdfs:label "has atom count" .
### https://rdf.metanetx.org/schema/atomElem
:atomElem rdf:type owl:DatatypeProperty ;
rdfs:domain :ElemFormula ;
rdfs:range xsd:string ;
rdfs:comment "Any atomic symbol or \"STAR\" is acceptable." ;
rdfs:isDefinedBy ;
rdfs:label "has atomic symbol" .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/charge
:charge rdf:type owl:DatatypeProperty ;
rdfs:domain :CHEM ;
rdfs:range xsd:integer ;
rdfs:comment "" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/chemCount
:chemCount rdf:type owl:DatatypeProperty ;
rdfs:domain :MNET ;
rdfs:range xsd:integer ;
rdfs:comment "Number of chemicals" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/chemInMNXref
:chemInMNXref rdf:type owl:DatatypeProperty ;
rdfs:domain :CHEM ;
rdfs:range xsd:boolean ;
rdfs:comment "identifies metabolites in MNXref" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/classification
:classification rdf:type owl:DatatypeProperty ;
rdfs:domain :REAC ;
rdfs:range xsd:string ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/compCount
:compCount rdf:type owl:DatatypeProperty ;
rdfs:domain :MNET ;
rdfs:range xsd:integer ;
rdfs:comment "Number of compartments" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/errorLog
:errorLog rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :logComment ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/errorLogReorderAtoms
:errorLogReorderAtoms rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorLog .
### https://rdf.metanetx.org/schema/errorSrc
:errorSrc rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/errorSrcCharge
:errorSrcCharge rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorSrc ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:integer .
### https://rdf.metanetx.org/schema/errorSrcInChI
:errorSrcInChI rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorSrc ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/errorSrcInChIKey
:errorSrcInChIKey rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorSrc ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/errorSrcMOL
:errorSrcMOL rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorSrc .
### https://rdf.metanetx.org/schema/errorSrcMolFormula
:errorSrcMolFormula rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorSrc .
### https://rdf.metanetx.org/schema/errorSrcMolWeight
:errorSrcMolWeight rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorSrc .
### https://rdf.metanetx.org/schema/errorStdSkip
:errorStdSkip rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/errorStructSkipped
:errorStructSkipped rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :errorLog ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/formula
:formula rdf:type owl:DatatypeProperty ;
rdfs:domain :CHEM ;
rdfs:range xsd:string ;
rdfs:comment "" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/inchi
:inchi rdf:type owl:DatatypeProperty ;
rdfs:domain :CHEM ;
rdfs:range xsd:string ;
rdfs:comment "" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/inchikey
:inchikey rdf:type owl:DatatypeProperty ;
rdfs:domain :CHEM ;
rdfs:range xsd:string ;
rdfs:comment "" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/isBalanced
:isBalanced rdf:type owl:DatatypeProperty ;
rdfs:domain :REAC ;
rdfs:range xsd:boolean ;
rdfs:comment "Is the reaction balanced?" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/isGenericComp
:isGenericComp rdf:type owl:DatatypeProperty ;
rdfs:domain :COMP ;
rdfs:range xsd:boolean ;
rdfs:comment "tags generic/placeholder compartment" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/isTransport
:isTransport rdf:type owl:DatatypeProperty ;
rdfs:domain :REAC ;
rdfs:range xsd:boolean ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/lineage
:lineage rdf:type owl:DatatypeProperty ;
rdfs:domain :MNET ;
rdfs:range xsd:string ;
rdfs:comment "Organism lineage" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/logComment
:logComment rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mass
:mass rdf:type owl:DatatypeProperty ;
rdfs:domain :CHEM ;
rdfs:range xsd:decimal ;
rdfs:comment "" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/mnxBondStereoString
:mnxBondStereoString rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxChiralStereoString
:mnxChiralStereoString rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxFormula
:mnxFormula rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxGlobalCharge
:mnxGlobalCharge rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:integer .
### https://rdf.metanetx.org/schema/mnxInChI
:mnxInChI rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxInChIKey
:mnxInChIKey rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxInChIKeyStd
:mnxInChIKeyStd rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxInChINonStd
:mnxInChINonStd rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxInChIStd
:mnxInChIStd rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxInChIkKeyNonStd
:mnxInChIkKeyNonStd rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxMOL
:mnxMOL rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/mnxMolWeight
:mnxMolWeight rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:double .
### https://rdf.metanetx.org/schema/mnxSMILES
:mnxSMILES rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/organism
:organism rdf:type owl:DatatypeProperty ;
rdfs:domain :MNET ;
rdfs:range xsd:string ;
rdfs:comment "Organism name" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/peptCount
:peptCount rdf:type owl:DatatypeProperty ;
rdfs:domain :MNET ;
rdfs:range xsd:integer ;
rdfs:comment "Number of genes/peptides" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/reacCount
:reacCount rdf:type owl:DatatypeProperty ;
rdfs:domain :MNET ;
rdfs:range xsd:integer ;
rdfs:comment "Number of reactions" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/reacInMNXref
:reacInMNXref rdf:type owl:DatatypeProperty ;
rdfs:domain :REAC ;
rdfs:range xsd:boolean ;
rdfs:comment "identifies reactions in MNXref" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/smiles
:smiles rdf:type owl:DatatypeProperty ;
rdfs:domain :CHEM ;
rdfs:range xsd:string ;
rdfs:comment "" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/srcCharge
:srcCharge rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:integer .
### https://rdf.metanetx.org/schema/srcFormula
:srcFormula rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/srcInChI
:srcInChI rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/srcInChIkey
:srcInChIkey rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/srcMOL
:srcMOL rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/srcMolWeight
:srcMolWeight rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:double .
### https://rdf.metanetx.org/schema/srcName
:srcName rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/srcSMILES
:srcSMILES rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/stdCharge
:stdCharge rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:integer .
### https://rdf.metanetx.org/schema/stdFormula
:stdFormula rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/stdInChI
:stdInChI rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/stdInChIKey
:stdInChIKey rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/stdMOL
:stdMOL rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/stdMolWeight
:stdMolWeight rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:double .
### https://rdf.metanetx.org/schema/stdMonoIsotopicMass
:stdMonoIsotopicMass rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:double .
### https://rdf.metanetx.org/schema/stdSMILES
:stdSMILES rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/structOrigin
:structOrigin rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/structureSource
:structureSource rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/warnLog
:warnLog rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :logComment ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/warnSrc
:warnSrc rdf:type owl:DatatypeProperty ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/warnSrcInChI
:warnSrcInChI rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :warnSrc ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
### https://rdf.metanetx.org/schema/warnSrcSMILES
:warnSrcSMILES rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :warnSrc .
### https://rdf.metanetx.org/schema/warnStructIsReplacedBy
:warnStructIsReplacedBy rdf:type owl:DatatypeProperty ;
rdfs:subPropertyOf :warnLog ;
rdfs:domain :ChemXRef ;
rdfs:range xsd:string .
#################################################################
# Classes
#################################################################
### http://purl.obolibrary.org/obo/CHEBI_24431
rdf:type owl:Class ;
owl:equivalentClass :ChemXRef ,
:MolStrucure .
### http://purl.obolibrary.org/obo/CHEBI_26519
rdf:type owl:Class ;
owl:equivalentClass :FreeRadical .
### http://purl.obolibrary.org/obo/CHEBI_60027
rdf:type owl:Class ;
owl:equivalentClass :Polymer .
### http://www.w3.org/1999/02/22-rdf-syntax-ns#Class
rdf:Class rdf:type owl:Class .
### http://www.w3.org/2000/01/rdf-schema#Property
rdfs:Property rdf:type owl:Class .
### 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/BioComplex
:BioComplex rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
rdfs:comment "A complex is a compound that features a bond between an atom of an organic molecule and a metal. Complex can convey a non-zero charge. Salt and complex form a continum, but a practical distinction can hopefully be established in the context of metabolic network. Complex implying abiotic metals are likely to be classified as salt." ;
rdfs:isDefinedBy ;
rdfs:label "A complex of biological origin" ;
;
;
:MolOntology .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/CHEM
:CHEM rdf:type owl:Class ;
rdfs:comment "A MetaNetX metabolite is defined as a collection of chemical entity identifiers gathered from external resources and mapped together because they refer to the same underlying compound." ;
rdfs:isDefinedBy ;
rdfs:label "MetaNetX metabolite class" .
### 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" ;
rdfs:isDefinedBy ;
rdfs:label "MetaNetX compartment, i.e. a set of sub-cellular compartments" .
### https://rdf.metanetx.org/schema/CPLX
:CPLX rdf:type owl:Class ;
rdfs:comment "The type for protein complexes" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/ChemXRef
:ChemXRef 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:isDefinedBy ;
rdfs:label "mnx:EMPTY " .
### https://rdf.metanetx.org/schema/ElemFormula
:ElemFormula rdf:type owl:Class ;
rdfs:comment "Instance of this class contains a single (atomic) symbol and a number (of atoms)" ;
rdfs:isDefinedBy ;
rdfs:label "Elemental composition" .
### https://rdf.metanetx.org/schema/FreeRadical
:FreeRadical rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
rdfs:comment "A free radical is a molecular entity possessing one or several unpaired electron." ;
rdfs:isDefinedBy ;
rdfs:label "free radical" .
### https://rdf.metanetx.org/schema/FullyDefinedStereo
:FullyDefinedStereo rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
owl:disjointWith :IncompleteStereo ,
:Symbol ;
rdfs:isDefinedBy ;
rdfs:label "A molecula entity with fully defined stereogenic atoms and bonds, or none of them. This concept is absent from the ChEBI ontology version 241." ,
"molecular entity with completly defined stereochemistry" .
### 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)" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/Generic
:Generic rdf:type owl:Class ;
rdfs:subClassOf :Incomplete ;
owl:disjointWith :Residue ;
rdfs:comment """
A molecular entity which structure contains one or several R groups.
Molecular weight and monoisotopic mass may or may not be available.
Distinction between mnx:Residue and mnx:Generic is sometimes difficult to delineate given available data.
In doubt mnx:Generic is assigned.
""" ;
rdfs:isDefinedBy ;
rdfs:label "generic" ;
.
### https://rdf.metanetx.org/schema/Incomplete
:Incomplete rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
rdfs:comment "A molecular structure which include a part that is not known or specified" ;
rdfs:isDefinedBy ;
rdfs:label "incomplete" .
### https://rdf.metanetx.org/schema/IncompleteStereo
:IncompleteStereo rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
owl:disjointWith :Symbol ;
rdfs:comment "A molecular entity containing some stereogenic atoms or double bonds, which stereochoistry is not fully defined. This concept is absent from the ChEBI ontology version 241." ;
rdfs:isDefinedBy ;
rdfs:label "molecular entity with incompletly defined stereochemistry" .
### https://rdf.metanetx.org/schema/MNET
:MNET rdf:type owl:Class ;
rdfs:comment "The type for metabolic network models" ;
rdfs:isDefinedBy .
### 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:isDefinedBy ;
rdfs:label "mnx:MNXR01" .
### https://rdf.metanetx.org/schema/MolCategory
:MolCategory rdf:type owl:Class .
### https://rdf.metanetx.org/schema/MolStrucure
:MolStrucure rdf:type owl:Class ;
rdfs:comment "A molecular entity, with a complete or partial structure, from which total charge and elementary formula can be computed." ;
rdfs:isDefinedBy ;
rdfs:label "Chemical entity with a chemical structure" ;
:MolOntology .
### https://rdf.metanetx.org/schema/MolSymbol
:MolSymbol rdf:type owl:Class ;
rdfs:comment """A chemical entity, with no explicit description of its molecular structure,
or with a structure that has been invalidated during MetaNetX MNXref computation.""" ;
rdfs:isDefinedBy ;
rdfs:label "A chemical symbol with no molecular structure, or an invalidated structure." ;
:MolOntology .
### https://rdf.metanetx.org/schema/MolSymbolDefined
:MolSymbolDefined rdf:type owl:Class ;
rdfs:subClassOf :MolSymbol ;
rdfs:comment "A chemical symbol which correspond to one or several chemical entities with defined molecular structures, but which explicit values are unknown in practice." ;
rdfs:isDefinedBy ;
rdfs:label "A chemical symbol with implicit molecular structures" ;
;
"chebi:132494 has definition \"Any polyunsaturated fatty acid containing 16 carbons and 2 double bonds\". A structure with an R group is given, but the description \"16 carbons and 2 double bonds\" pertains to the R group. Hence the given structure is almost uninformative." .
### https://rdf.metanetx.org/schema/MolSymbolUndefined
:MolSymbolUndefined rdf:type owl:Class ;
rdfs:subClassOf :MolSymbol ;
rdfs:isDefinedBy ;
rdfs:label "A chemical symbol with no molecular structure, charge and formula. These can be completely unknown and possibly variable. " ;
:BIOMASS ;
:MolOntology ;
"Biomass elementary composition is variable." .
### https://rdf.metanetx.org/schema/MolUnknown
:MolUnknown rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
rdfs:comment "A placeholder class for molecules with no information at all. It should be never appear in a perfect world, but the world is not perfect." ;
rdfs:isDefinedBy ;
rdfs:label "unknown molecule" .
### 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" ;
rdfs:isDefinedBy .
### 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" ;
rdfs:isDefinedBy .
### https://rdf.metanetx.org/schema/Polymer
:Polymer rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
rdfs:comment "A molecular entity with SGroup (poylmeric) notations. This definition is very broad." ;
rdfs:isDefinedBy ;
rdfs:label "polymer" ;
:Ontology .
### 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)" ;
rdfs:isDefinedBy ;
rdfs:label "MetaNetX reaction, i.e. a set of chemical reaction" .
### https://rdf.metanetx.org/schema/RGroup
:RGroup rdf:type owl:Class .
### https://rdf.metanetx.org/schema/RGroup_excluded
:RGroup_excluded rdf:type owl:Class ;
rdfs:subClassOf :RGroup ;
owl:disjointWith :RGroup_included ,
:RGroup_unknown ;
rdfs:comment "R groups are excluded from molecular weight and monoisotopic mass." ;
rdfs:isDefinedBy ;
rdfs:label "R group excluded" ;
.
### https://rdf.metanetx.org/schema/RGroup_included
:RGroup_included rdf:type owl:Class ;
rdfs:subClassOf :RGroup ;
owl:disjointWith :RGroup_unknown ;
rdfs:comment "R group are included in molecular weight, monoisotopic mass and formula." ;
rdfs:isDefinedBy ;
rdfs:label "R group included" .
### https://rdf.metanetx.org/schema/RGroup_unknown
:RGroup_unknown rdf:type owl:Class ;
rdfs:subClassOf :RGroup ;
rdfs:comment "It is not known if R group are included in molecular weight and monoisotopic mass." ;
rdfs:isDefinedBy ;
rdfs:label "R group UNKNOWN" .
### https://rdf.metanetx.org/schema/Residue
:Residue rdf:type owl:Class ;
rdfs:subClassOf :Incomplete ;
rdfs:comment "At least one star atom is present, and it is not included in molecular weight and monoisotopic mass calculation." ;
rdfs:isDefinedBy ;
rdfs:label "residue" ;
.
### https://rdf.metanetx.org/schema/Salt
:Salt rdf:type owl:Class ;
rdfs:subClassOf :ChemXRef ;
rdfs:comment "A salt is an assembly of cations and anion in fixed proportion, usually with a zero overall charge. Salt and complex form a continum, but a practical distinction can hopefully be established in the context of metabolic network." ;
rdfs:isDefinedBy ;
rdfs:label "salt" ;
;
;
:MolOntology .
### https://rdf.metanetx.org/schema/Symbol
:Symbol rdf:type owl:Class .
### https://rdf.metanetx.org/schema/chemXref
:chemXref rdf:type owl:Class .
#################################################################
# 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:isDefinedBy ;
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:isDefinedBy ;
rdfs:label "mnx:BOUNDARY" .
### https://rdf.metanetx.org/schema/ChemXRef
:ChemXRef rdf:type owl:NamedIndividual ,
rdf:Class .
### 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:isDefinedBy ;
rdfs:label "mnx:HYDROXYDE" .
### https://rdf.metanetx.org/schema/LB
:LB rdf:type owl:NamedIndividual ,
rdfs:Resource ;
rdfs:comment "Symbol for default lower bound" ;
rdfs:label "mnx:LB" .
### 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:isDefinedBy ;
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:isDefinedBy ;
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:isDefinedBy ;
rdfs:label "mnx:SPONTANEOUS" .
### https://rdf.metanetx.org/schema/UB
:UB rdf:type owl:NamedIndividual ,
rdfs:Resource ;
rdfs:comment "Symbol for default upper bound" ;
rdfs:label "mnx:UB" .
### https://rdf.metanetx.org/schema/WATER
:WATER rdf:type owl:NamedIndividual ,
:CHEM ;
rdfs:comment "A symbol to represent water" ;
rdfs:isDefinedBy ;
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/errorLog
:errorLog rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorLogReorderAtoms
:errorLogReorderAtoms rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorSrc
:errorSrc rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorSrcCharge
:errorSrcCharge rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorSrcInChI
:errorSrcInChI rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorSrcInChIKey
:errorSrcInChIKey rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorSrcMOL
:errorSrcMOL rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorSrcMolFormula
:errorSrcMolFormula rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorSrcMolWeight
:errorSrcMolWeight rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorStdSkip
:errorStdSkip rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/errorStructSkipped
:errorStructSkipped rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/hasIsomericChild
:hasIsomericChild rdf:type owl:NamedIndividual .
### https://rdf.metanetx.org/schema/logComment
:logComment rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxBondStereoString
:mnxBondStereoString rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxChiralStereoString
:mnxChiralStereoString rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxFormula
:mnxFormula rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxGlobalCharge
:mnxGlobalCharge rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxInChI
:mnxInChI rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxInChIKey
:mnxInChIKey rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxInChIKeyStd
:mnxInChIKeyStd rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxInChINonStd
:mnxInChINonStd rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxInChIStd
:mnxInChIStd rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxInChIkKeyNonStd
:mnxInChIkKeyNonStd rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxMOL
:mnxMOL rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxMolWeight
:mnxMolWeight rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/mnxSMILES
:mnxSMILES rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcCharge
:srcCharge rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcFormula
:srcFormula rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcInChI
:srcInChI rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcInChIkey
:srcInChIkey rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcMOL
:srcMOL rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcMolWeight
:srcMolWeight rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcName
:srcName rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/srcSMILES
:srcSMILES rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdCharge
:stdCharge rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdFormula
:stdFormula rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdInChI
:stdInChI rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdInChIKey
:stdInChIKey rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdMOL
:stdMOL rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdMolWeight
:stdMolWeight rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdMonoIsotopicMass
:stdMonoIsotopicMass rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/stdSMILES
:stdSMILES rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/structIsReplacedBy
:structIsReplacedBy rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/structOrigin
:structOrigin rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/structureDerivedFrom
:structureDerivedFrom rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/structureSource
:structureSource rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/warnLog
:warnLog rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/warnSrc
:warnSrc rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/warnSrcInChI
:warnSrcInChI rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/warnSrcSMILES
:warnSrcSMILES rdf:type owl:NamedIndividual ,
rdfs:Property .
### https://rdf.metanetx.org/schema/warnStructIsReplacedBy
:warnStructIsReplacedBy rdf:type owl:NamedIndividual ,
rdfs:Property .
#################################################################
# Annotations
#################################################################
:ChemXRef rdfs:comment """An instance of this class is an identifier of a chemical entity.
A few chemical entity are defined by MetaNetX, but the vast majority of them an imported from external resources database.
This class is also the top node of the MetaNetX simple ontology for chemical symbols and entities.
Its primary purpose is to support
metabolic resconstruction.
It is not meant to become chemical ontology like ChEBI.
""" ;
rdfs:isDefinedBy ;
rdfs:label "chemical entity class" .
: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" ;
rdfs:isDefinedBy ;
rdfs:label "has stereo child" .
:chemXref rdfs:comment "A predicate to list all public IRIs that are included in a MNXref metabolite" ;
rdfs:isDefinedBy ;
rdfs:label "contains chem member" .
:errorLog rdfs:isDefinedBy ;
rdfs:label "error detected while process molecular structures" ,
"error detected while process molecular structures, that affects the produced data" .
:errorLogReorderAtoms rdfs:isDefinedBy ;
rdfs:label "error while reordering atoms" .
:errorSrc rdfs:isDefinedBy ;
rdfs:label "error detected while importing the raw source from source" .
:errorSrcCharge rdfs:isDefinedBy ;
rdfs:label "error detected while importing source charge" .
:errorSrcInChI rdfs:isDefinedBy ;
rdfs:label "error detected while importing source InChI" .
:errorSrcInChIKey rdfs:isDefinedBy ;
rdfs:label "error detected while importing source InChIKey" .
:errorSrcMOL rdfs:isDefinedBy ;
rdfs:label "error detected while importing source MOL" .
:errorSrcMolFormula rdfs:isDefinedBy ;
rdfs:label "error detected while parsing source Mol Formula" .
:errorSrcMolWeight rdfs:isDefinedBy ;
rdfs:label "error detected while importing source Mol Weight" .
:errorStdSkip rdfs:isDefinedBy ;
rdfs:label "error during standardization, entry skipped" .
:errorStructSkipped rdfs:isDefinedBy ;
rdfs:label "chem struct processing was skipped (manual curation)" .
:hasIsomericChild rdfs:isDefinedBy ;
owl:deprecated "true"^^xsd:boolean .
:logComment rdfs:isDefinedBy ;
rdfs:label "specific comment produced while processing molecular structures" .
:mnxBondStereoString rdfs:isDefinedBy ;
rdfs:label "has bond stereo string" .
:mnxChiralStereoString rdfs:isDefinedBy ;
rdfs:label "has chiral stereo string" .
:mnxFormula rdfs:isDefinedBy ;
rdfs:label "has formula" .
:mnxGlobalCharge rdfs:isDefinedBy ;
rdfs:label "has global charge" .
:mnxInChI rdfs:isDefinedBy ;
rdfs:label "has MNX InChI" .
:mnxInChIKey rdfs:isDefinedBy ;
rdfs:label "has MNX InChI key" .
:mnxInChIKeyStd rdfs:isDefinedBy ;
rdfs:label "has standard InChI key" .
:mnxInChINonStd rdfs:isDefinedBy ;
rdfs:label "has non-standard InChI" .
:mnxInChIStd rdfs:isDefinedBy ;
rdfs:label "has standard InChI" .
:mnxInChIkKeyNonStd rdfs:isDefinedBy ;
rdfs:label "has non-standard InChI key" .
:mnxMOL rdfs:isDefinedBy ;
rdfs:label "has MNX MOL" .
:mnxMolWeight rdfs:isDefinedBy ;
rdfs:label "has molecular weight" .
:mnxSMILES rdfs:isDefinedBy ;
rdfs:label "has SMILES" .
:reacIsom rdfs:comment "The object reaction has a more detailed description of the stereochemistry of its reactants than the subject reaction" .
:srcCharge rdfs:isDefinedBy ;
rdfs:label "has imported charge" .
:srcFormula rdfs:isDefinedBy ;
rdfs:label "has imported formula" .
:srcInChI rdfs:isDefinedBy ;
rdfs:label "has imported InChI" .
:srcInChIkey rdfs:isDefinedBy ;
rdfs:label "has imported InChIkey" .
:srcMOL rdfs:isDefinedBy ;
rdfs:label "has imported MOL entry" .
:srcMolWeight rdfs:isDefinedBy ;
rdfs:label "has imported molecular weight" .
:srcName rdfs:isDefinedBy ;
rdfs:label "has imported name(s)" .
:srcSMILES rdfs:isDefinedBy ;
rdfs:label "has imported SMILES" .
:stdCharge rdfs:isDefinedBy ;
rdfs:label "has global charge" .
:stdFormula rdfs:isDefinedBy ;
rdfs:label "has formula" .
:stdInChI rdfs:isDefinedBy ;
rdfs:label "has standard InChI" .
:stdInChIKey rdfs:isDefinedBy ;
rdfs:label "has standard InChI key" .
:stdMOL rdfs:isDefinedBy ;
rdfs:label "has standard MOL" .
:stdMolWeight rdfs:isDefinedBy ;
rdfs:label "has molecular weight" .
:stdMonoIsotopicMass rdfs:isDefinedBy ;
rdfs:label "has monoisotopic mass" .
:stdSMILES rdfs:isDefinedBy ;
rdfs:label "has SMILES" .
:structIsReplacedBy rdfs:comment """This indicates that the structure of the subject chemical
entity is replaced by the structure of the object chemical entity. This patch
is manually curated to correct errors or to fill missing structures in MetaNetX.""" ;
rdfs:isDefinedBy ;
rdfs:label "structure is replaced by" .
:structOrigin rdfs:isDefinedBy ;
rdfs:label "origin of structure data" .
:structureDerivedFrom rdf:comment "Structural information was obtained from the object entry" ;
rdfs:isDefinedBy ;
rdfs:label "has structure derived from" .
:structureSource rdfs:comment "Structural information is recomputed from a single source in the MetaNetX pipeline. The selected source is indicated by this predicate. It can take values \"patch\", \"MOL\", \"SMILES\", \"InChI\", \"none\" in the order of source preferences, i.e. the first available source was selected." ;
rdfs:isDefinedBy ;
rdfs:label "has structure from source type" .
:warnLog rdfs:isDefinedBy ;
rdfs:label "warning produced while process molecular structures, that does not affect the produced data" .
:warnSrc rdfs:isDefinedBy ;
rdfs:label "warning produced while importing source data" .
:warnSrcInChI rdfs:isDefinedBy ;
rdfs:label "warning produced while importing source InChIKey" .
:warnSrcSMILES rdfs:isDefinedBy ;
rdfs:label "warning produced while importing source SMILES" .
:warnStructIsReplacedBy rdfs:comment "This provides additional information on the structure replacement" ;
rdfs:isDefinedBy ;
rdfs:label "comment on structure replacement" .
### Generated by the OWL API (version 5.1.18) https://github.com/owlcs/owlapi/