@prefix : <https://w3id.org/emi/abox#> .
@prefix sw: <http://www.w3.org/2003/06/sw-vocab-status/ns#> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix wd: <http://www.wikidata.org/entity/> .
@prefix emi: <https://w3id.org/emi#> .
@prefix npc: <https://w3id.org/emi/npc#> .
@prefix org: <http://www.w3.org/ns/org#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sdo: <http://schema.org/> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix bibo: <http://purl.org/ontology/bibo/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix obda: <https://w3id.org/obda/vocabulary#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix qudt: <http://qudt.org/schema/qudt/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix sosa: <http://www.w3.org/ns/sosa/> .
@prefix vann: <http://purl.org/vocab/vann/> .
@prefix voaf: <http://purl.org/vocommons/voaf#> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix orcid: <http://orcid.org/> .
@prefix widoco: <https://w3id.org/widoco/vocab#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> .
@base <https://w3id.org/emi/abox#> .

<https://w3id.org/emi> rdf:type owl:Ontology ;
                        owl:versionIRI <https://w3id.org/emi/version/1.0> ;
                        owl:imports <http://www.w3.org/2004/02/skos/core> ,
                                    <http://www.w3.org/ns/prov-o-20130430> ,
                                    sosa: ,
                                    <https://w3id.org/emi/npc> ,
                                    dcterms: ,
                                    geo: ;
                        dcterms:abstract "The Earth Metabolome Initiative ontology is mainly designed as data schema to structure and describe natural product taxonomy, spectrum annotation provenance, sample and observation data, mass spectrometry data and analysis, and chemical structure representations. The EMI ontology replaces the [ENPKG vocabulary](https://enpkg.commons-lab.org/doc/index.html)." ;
                        dcterms:bibliographicCitation "The Earth Metabolome Initiative Consortium. The Earth Metabolome Initiative (EMI) ontology. Revision: 1.0. Retrieved from: https://w3id.org/emi/version/1.0" ;
                        dcterms:contributor <https://orcid.org/0000-0001-9292-9463> ,
                                            <https://orcid.org/0000-0002-3648-7362> ,
                                            <https://orcid.org/0000-0002-9619-1707> ,
                                            <https://orcid.org/0000-0003-3389-2191> ,
                                            <https://orcid.org/0000-0002-1269-2038> ,
                                            <https://orcid.org/0000-0002-3175-5372> ,
                                            <https://orcid.org/0000-0003-3213-4495> ,
                                            <https://orcid.org/0009-0005-5515-1230>;
                        dcterms:created "2023-11-02"^^xsd:date ;
                        dcterms:creator <https://orcid.org/0000-0002-3175-5372> ;
                        dcterms:description "The Earth Metabolome Initiative (EMI) ontology is designed to capture and structure the metabolic content of all currently known species on our planet."@en ;
                        dcterms:issue "2024-04-03"^^xsd:date ;
                        dcterms:license <https://creativecommons.org/publicdomain/zero/1.0> ;
                        dcterms:modified "2025-07-15"^^xsd:date ;
                        dcterms:publisher <https://www.earthmetabolome.org> ;
                        dcterms:replaces <https://purl.org/emi/version/0.3> ;
                        dcterms:title "The Earth Metabolome Initiative (EMI) ontology"@en ;
                        bibo:status <http://purl.org/ontology/bibo/status/draft> ;
                        vann:preferredNamespacePrefix "emi" ;
                        vann:preferredNamespaceUri emi: ;
                        sdo:codeRepository "https://github.com/earth-metabolome-initiative/earth_metabolome_ontology"^^xsd:anyURI ;
                        sdo:image <https://www.earthmetabolome.org/earth_metabolome_ontology/images/EMI-diagram.png> ;
                        rdfs:seeAlso <https://bioschemas.org> ,
                                     <https://schema.org> ,
                                     <https://enpkg.commons-lab.org/doc/index.html> ;
                        owl:versionInfo "1.0" ;
                        foaf:logo <https://www.earthmetabolome.org/earth_metabolome_ontology/images/logo.png> ;
                        widoco:introduction """The Earth Metabolome Initiative (EMI) ontology replaces the Experimental Natural Products Knowledge Graph [(ENPKG) vocabulary]( https://enpkg.commons-lab.org/doc/index.html). The EMI ontology is used to structure spectrum annotation provenance by reusing the [PROV-O ontology](https://www.w3.org/TR/prov-o/) (a W3C recommendation) and sample and observation data by applying the [SOSA ontology](https://www.w3.org/TR/vocab-ssn/). EMI reuses the SOSA ontology as a data schema for struturing the Sample and Observation data. SOSA (Sensor, Observation, Sample, and Actuator) is a subset of SSN (Semantic Sensor Network Ontology) that is a W3C recommendation. Although, the SSN was developed with ontology engineers in mind as the primary audience. They addressed changes in scope and audience that currently also includes scientific observations that may make heavy use of sampling strategies, and, therefore, the Sampling, Sampler, and Sample classes, as well as their corresponding properties, have been added to SOSA and SSN. Chemical taxonomy is also highly structure in EMI by relying on a taxonomy derived from NPClassifier (i.e., EMI imports [Natural Product Classifier vocabulary](https://w3id.org/emi/npc)). This taxonomy was defined for EMI with the [SKOS vocabulary](https://www.w3.org/TR/skos-reference). Indeed, it is an SKOS-based vocabulary for the structural classification of natural products. The skos:broder term is used to represent the hierarchy among Classes, Superclasses and Pathways.  npc:Class, npc:Superclass and npc:Pathway are subclasses of skos:Concept. rdfs:label is assigned for each term of the taxonomy that are instances of one of the subclasses of skos:Concept.

SOSA reuse. We consider a Mass Spectrometer as a sosa:Platform. The MS detector that belongs to a Mass Spectrometer is a Sensor. If we do not want to capture the equipment (Mass Spectrometer for provenance) of the generated analysis such as by Liquid chromatography–mass spectrometry (LCMS), we can ignore/ommit it. The observation is interpreted as a prov:Activity/sosa:Observation/emi:Analysis (the Analysis as defined in the Earth Metabolome Intiative model). This observation (a.k.a. LCMS Analysis) uses (prov:use/sosa:hasFeatureOfInterest) some sample. This sample comes from some emi:System (e.g., species or another sample like a Raw Material, a broader specimen). All EMI model classes related to samples are subclasses of sosa:Sample, notably emi:Aliquot, emi:Blank, emi:ExtractSample, emi:RawMaterial and emi:QCSample.

We can classify each Specimen by using some Specimen taxonomy, for example, [specimenType](https://isamplesorg.github.io/models/generated/vocabularies/specimenType.html) that relies on SKOS. Moreover, we can also classify a sample with an external material taxonomy (e.g.,  [materialType](https://isamplesorg.github.io/models/generated/vocabularies/materialType.html#organicmaterial)). The raw material (emi:RawMaterial) is also a sosa:sample. In case it is needed to describe the \"Mass Spectrometer\" as a sampler too, we can apply the sosa:Sampler class to define it. The sampling process resuts on subsamples (e.g., emi:Aliquot). The extracted sample can be classified with an external taxonomy (e.g., an Specimen taxonomy) with the term emi:isClassifiedWith.

Other metabolomics data are structured with specific EMI classes such as emi:ChemicalStrucutre for represeting molecules, emi:MS2Spectrum for the mass spectrometry (MS2 spectra), emi:LCMSFeatureSet that represents features obtained from the processing of a given LCMS analysis, please refer to classes and properties descriptions. """ .

#################################################################
#    Annotation properties
#################################################################

###  http://purl.org/dc/elements/1.1/date
<http://purl.org/dc/elements/1.1/date> rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/elements/1.1/description
<http://purl.org/dc/elements/1.1/description> rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/elements/1.1/title
<http://purl.org/dc/elements/1.1/title> rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/bibliographicCitation
dcterms:bibliographicCitation rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/contributor
dcterms:contributor rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/creator
dcterms:creator rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/description
dcterms:description rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/issued
dcterms:issued rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/license
dcterms:license rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/publisher
dcterms:publisher rdf:type owl:AnnotationProperty .


###  http://purl.org/dc/terms/replaces
dcterms:replaces rdf:type owl:AnnotationProperty ;
                 dcterms:description "This property is intended to be used with non-literal values. This property is an inverse property of Is Replaced By."@en ;
                 dcterms:issued "2000-07-11"^^xsd:date ;
                 rdfs:comment "A related resource that is supplanted, displaced, or superseded by the described resource."@en ;
                 rdfs:isDefinedBy dcterms: ;
                 rdfs:label "Replaces"@en .


###  http://purl.org/dc/terms/title
dcterms:title rdf:type owl:AnnotationProperty .


###  http://purl.org/vocab/vann/example
vann:example rdf:type owl:AnnotationProperty .


###  http://purl.org/vocab/vann/preferredNamespacePrefix
vann:preferredNamespacePrefix rdf:type owl:AnnotationProperty .


###  http://purl.org/vocab/vann/preferredNamespaceUri
vann:preferredNamespaceUri rdf:type owl:AnnotationProperty .


###  http://schema.org/image
sdo:image rdf:type owl:AnnotationProperty .




###  http://www.w3.org/2004/02/skos/core#altLabel
skos:altLabel rdf:type owl:AnnotationProperty ;
              rdfs:comment "The range of skos:altLabel is the class of RDF plain literals."@en ,
                           "skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties."@en ;
              rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
              rdfs:label "alternative label"@en ;
              skos:definition "An alternative lexical label for a resource."@en ;
              skos:example "Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel)."@en ;
              rdfs:subPropertyOf rdfs:label .


###  http://www.w3.org/2004/02/skos/core#definition
skos:definition rdf:type owl:AnnotationProperty .


###  http://www.w3.org/2004/02/skos/core#example
skos:example rdf:type owl:AnnotationProperty .


###  http://www.w3.org/2004/02/skos/core#prefLabel
skos:prefLabel rdf:type owl:AnnotationProperty ;
               rdfs:comment "A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag."@en ,
                            "The range of skos:prefLabel is the class of RDF plain literals."@en ,
                            """skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise
      disjoint properties."""@en ;
               rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
               rdfs:label "preferred label"@en ;
               skos:definition "The preferred lexical label for a resource, in a given language."@en ;
               rdfs:subPropertyOf rdfs:label .


###  http://xmlns.com/foaf/0.1/based_near
foaf:based_near rdf:type owl:AnnotationProperty .


###  http://xmlns.com/foaf/0.1/logo
foaf:logo rdf:type owl:AnnotationProperty .


###  https://w3id.org/emi#hasIonization
emi:hasIonization rdf:type owl:AnnotationProperty ;
                  rdfs:range xsd:string .


#################################################################
#    Datatypes
#################################################################

###  http://www.w3.org/2001/XMLSchema#date
xsd:date rdf:type rdfs:Datatype .


#################################################################
#    Object Properties
#################################################################

###  http://purl.uniprot.org/core/rank
up:rank rdf:type owl:ObjectProperty ;
        rdfs:domain up:Taxon ;
        rdfs:range up:Rank ;
        rdfs:comment "The rank of a taxon." ;
        rdfs:isDefinedBy up: ;
        rdfs:label "rank" .




###  http://www.w3.org/ns/sosa/hasResult
sosa:hasResult vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix sosa: <http://www.w3.org/ns/sosa/> .
:VGF153_A02_neg.mzXML  rdf:type emi:LCMSAnalysisNeg, emi:LCMSAnalysis, sosa:Observation ;
                       sosa:hasResult :VGF153_A02_lcms_feature_list_neg .
:VGF153_A02_lcms_feature_list_neg rdf:type emi:LCMSFeatureSet.""" .


###  http://xmlns.com/foaf/0.1/depiction
foaf:depiction rdf:type owl:ObjectProperty ;
               rdfs:comment "http://www.simolecule.com/cdkdepict/depict/bow/svg?smi=CCCCCCCCCCCC%5BC%40%40H%5D(O)%5BC%40H%5D1CCC(C2CCC(CC(O)CCCCC%5BC%40%40H%5D(O)CC3%3DC%5BC%40H%5D(C)OC3%3DO)O2)O1&zoom=2.0&annotate=cip" .


###  https://w3id.org/emi#hasAnatomicalEntity
emi:hasAnatomicalEntity rdf:type owl:ObjectProperty ;
                        rdfs:domain sosa:Sample ;
                        rdfs:range emi:AnatomicalEntity ;
                        rdfs:label "has anatomical entity"@en ;
                        rdfs:comment "It can be used to assign an anatomical entity (e.g., body parts) to a source and/or target organism sample in an interaction system such as GloBI. When applicable, we recommend to state UBERON vocabulary anatomical entity terms." .


###  https://w3id.org/emi#hasAnnotation
emi:hasAnnotation rdf:type owl:ObjectProperty ;
                  rdfs:domain emi:MS2Spectrum ;
                  rdfs:range emi:SpectrumAnnotation ;
                  rdfs:label "has annotation" .


###  https://w3id.org/emi#hasChemicalStructure
emi:hasChemicalStructure rdf:type owl:ObjectProperty ;
                         rdfs:domain emi:StructuralAnnotation ;
                         rdfs:range emi:ChemicalStructure ;
                         rdfs:comment "Recommendation: prefer the chemical structure representation 2D InChIKey that also represents a collection of InChIKeys (i.e. chemicals) with common attributes. As a result, we can reduce the number of triples and redundacy to represent the same information that are common to many chemicals." ;
                         rdfs:label "has chemical structure representation" .


###  https://w3id.org/emi#hasClass
emi:hasClass rdf:type owl:ObjectProperty ;
             rdfs:subPropertyOf emi:isClassifiedWith ;
             rdfs:domain [ rdf:type owl:Class ;
                           owl:unionOf ( emi:ChemicalStructure
                                         emi:ChemicalTaxonAnnotation
                                       )
                         ] ;
             rdfs:range npc:Class ;
             owl:propertyDisjointWith emi:hasSuperClass ;
             vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix npc: <https://w3id.org/emi/npc#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:hasClass \"npc:CADINANE_SESQUITERPENOIDS\" .""" ;
             rdfs:label "has class" .


###  https://w3id.org/emi#hasConsensusSpectrum
emi:hasConsensusSpectrum rdf:type owl:ObjectProperty ;
                         rdfs:subPropertyOf emi:hasSpectrum ;
                         rdf:type owl:FunctionalProperty ;
                         rdfs:domain emi:LCMSFeature ;
                         rdfs:range emi:GNPSConsensusSpectrum ;
                         rdfs:label "has consensus spectrum" .


###  https://w3id.org/emi#hasDevelopmentalStage
emi:hasDevelopmentalStage rdf:type owl:ObjectProperty ;
                          rdfs:domain sosa:Sample ;
                          rdfs:range emi:DevelopmentalStage ;
                          rdfs:comment "The source or target organism sample of an interaction system such as GloBI can have a developmental stage." ;
                          rdfs:label "has developmental stage"  .


###  https://w3id.org/emi#hasFBMNComponent
emi:hasFBMNComponent rdf:type owl:ObjectProperty ;
                     rdfs:domain emi:LCMSFeature ;
                     vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasFBMNComponent :VGF153_A02_fbmn_neg_componentindex_0 .""" ;
                     rdfs:comment "Feature-based molecular network component." ;
                     rdfs:label "has FBMN component" .


###  https://w3id.org/emi#hasFirstMember
emi:hasFirstMember rdf:type owl:ObjectProperty ;
                   rdfs:subPropertyOf emi:hasPairMember ;
                   rdf:type owl:FunctionalProperty ;
                   rdfs:domain emi:LFpair ;
                   rdfs:range emi:LCMSFeature ;
                   rdfs:comment "The first member of a spectral pair." ;
                   rdfs:label "has first member" .


###  https://w3id.org/emi#hasInChIKey
emi:hasInChIKey rdf:type owl:ObjectProperty ;
                rdfs:subPropertyOf owl:topObjectProperty ;
                owl:inverseOf emi:isInChIKeyOf ;
                rdfs:domain [ rdf:type owl:Class ;
                              owl:unionOf ( emi:Chemical
                                            emi:SpectrumAnnotation
                                          )
                            ] ;
                rdfs:range emi:InChIKey ;
                owl:propertyChainAxiom ( emi:hasChemicalStructure
                                         emi:isInChIKey2DOf
                                       ) ;
                vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix wd: <http://www.wikidata.org/entity/> .
wd:Q27145340 rdf:type emi:Chemical ;
            dcterms:identifier \"Q27145340\" ;
            emi:hasInChIKey :ZCCLDKGWJIREQF-PDBXOOCHSA-N .""" ;
                rdfs:comment "It can be used to assign an InChIKey either to a chemical or to an spectrum annotation." ;
                rdfs:label "has InChIKey" .


###  https://w3id.org/emi#hasInChIKey2D
emi:hasInChIKey2D rdf:type owl:ObjectProperty ;
                  rdfs:subPropertyOf owl:topObjectProperty ;
                  owl:inverseOf emi:isInChIKey2DOf ;
                  rdf:type owl:FunctionalProperty ;
                  rdfs:domain emi:InChIKey ;
                  rdfs:range emi:InChIKey2D ;
                  vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix wd: <http://www.wikidata.org/entity/> .
:ZCCLDKGWJIREQF-PDBXOOCHSA-N  rdf:type emi:InChIKey ;
            emi:hasInChIKey2D :ZCCLDKGWJIREQF .""" ;
                  rdfs:comment "It can be used to represent the InChIKey2D of an emi:InChIKey that is chemical structure." ;
                  rdfs:label "has InChIKey2D" .


###  https://w3id.org/emi#hasLCMS
#emi:hasLCMS rdf:type owl:ObjectProperty ,
#                     owl:FunctionalProperty ;
#            rdfs:domain sosa:Sample ;
#            rdfs:range emi:LCMSAnalysis ;
#            rdfs:label "has LCMS analysis" ;
#            owl:deprecated "replaced by sosa:isFeatureOfInterestOf and its inverse property sosa:hasFeatureOfInterest" .


###  https://w3id.org/emi#hasLCMSFeature
emi:hasLCMSFeature rdf:type owl:ObjectProperty ;
                   rdfs:subPropertyOf emi:hasSpectrum ;
                   rdfs:domain emi:LCMSFeatureSet ;
                   rdfs:range emi:LCMSFeature ;
                   vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
:VGF153_A02_lcms_feature_list_neg rdf:type emi:LCMSFeatureSet ;
            emi:hasLCMSFeature usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A1 .""" ;
                   rdfs:comment "It relates a LCMS feature set to a feature." ;
                   rdfs:label "has LCMS feature" .


###  https://w3id.org/emi#hasLCMSFeatureSet
emi:hasLCMSFeatureSet rdf:type owl:ObjectProperty ;
                      rdfs:subPropertyOf sosa:hasResult ;
                      rdfs:domain emi:LCMSAnalysis ;
                      rdfs:range emi:LCMSFeatureSet ;
                      vann:example """@prefix emi: <https://w3id.org/emi#> .
:VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysis ;
            emi:hasLCMSFeatureSet :VGF153_A02_lcms_feature_list_neg .""" ;
                      rdfs:comment "It relates a LCMS analysis to a set of features." ;
                      rdfs:label "has LCMS feature set" .


###  https://w3id.org/emi#hasLabProcess
#emi:hasLabProcess rdf:type owl:ObjectProperty ;
#                  rdfs:domain emi:RawMaterial ;
#                  rdfs:range emi:ExtractSample ;
#                  rdfs:comment "The resulted extract after performing a sampling (e.g., a lab process)." ;
#                  rdfs:label "has processed sample" ;
#                  owl:deprecated "replaced by \"sosa:hasSample\" and its inverse property \"sosa:isSampleOf\"" .


###  https://w3id.org/emi#hasMassiveDOI
emi:hasMassiveDOI rdf:type owl:ObjectProperty ;
                  rdfs:domain emi:LCMSAnalysis ;
                  vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
:VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysis ;
            emi:hasMassiveDOI <https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000087728> .""" ;
                  rdfs:comment "It assigns a Massive repository DOI to a LCMS Analysis." ;
                  rdfs:label "has Massive DOI." .


###  https://w3id.org/emi#hasPairMember
emi:hasPairMember rdf:type owl:ObjectProperty ;
                  rdfs:domain emi:SpectralPair ;
                  rdfs:range emi:MS2Spectrum ;
                  rdfs:comment "LCMSFeature" ;
                  rdfs:label "has pair member" .


###  https://w3id.org/emi#hasPathway
emi:hasPathway rdf:type owl:ObjectProperty ;
               rdfs:subPropertyOf emi:isClassifiedWith ;
               rdfs:domain [ rdf:type owl:Class ;
                             owl:unionOf ( emi:ChemicalStructure
                                           emi:ChemicalTaxonAnnotation
                                         )
                           ] ;
               rdfs:range npc:Pathway ;
               vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix npc: <https://w3id.org/emi/npc#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:hasPathway npc:TERPENOIDS .""" ;
               rdfs:label "has pathway" .


###  https://w3id.org/emi#hasPhysiologicalStage
emi:hasPhysiologicalStage rdf:type owl:ObjectProperty ;
                          rdfs:domain sosa:Sample  ;
                          rdfs:range emi:PhysiologicalStage ;
                          rdfs:comment "It can be used to assign a physiological stage to a source and/or target organism sample in an interaction system such as GloBI. When applicable, we recommend to state PATO vocabulary anatomical entity terms." ;
                          rdfs:label "has physiological stage" .


###  https://w3id.org/emi#hasSecondMember
emi:hasSecondMember rdf:type owl:ObjectProperty ;
                    rdfs:subPropertyOf emi:hasPairMember ;
                    rdf:type owl:FunctionalProperty ;
                    rdfs:domain emi:LFpair ;
                    rdfs:range emi:LCMSFeature ;
                    rdfs:comment "The second member of a spectral pair." ;
                    rdfs:label "has second member" .


###  https://w3id.org/emi#hasSex
emi:hasSex rdf:type owl:ObjectProperty ;
           rdfs:domain [    rdf:type owl:Class ;
                            owl:unionOf (   emi:Organism
                                            emi:OrganismGroup )
                              ] ;
           rdfs:range emi:BiologicalSex ;
           rdfs:label "has sex" ;
           rdfs:comment "It can be used to assign a biological sex to a source and/or target organism sample in an interaction system such as GloBI. When applicable, we recommend to state PATO vocabulary biological sex terms." .


###  https://w3id.org/emi#hasSpec2VecDoc
emi:hasSpec2VecDoc rdf:type owl:ObjectProperty ;
                   rdfs:subPropertyOf owl:topObjectProperty ;
                   rdfs:domain emi:LCMSFeature ;
                   rdfs:range emi:Spec2VecDoc ;
                   vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasSpec2VecDoc :spec2vec_doc_mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 .""" ;
                   rdfs:label "has spec2vec documentation" .


###  https://w3id.org/emi#hasSpectrum
emi:hasSpectrum rdf:type owl:ObjectProperty ;
                rdfs:range emi:MS2Spectrum ;
                vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
:VGF153_A02_lcms_feature_list_neg rdf:type emi:LCMSFeatureSet ;
            emi:hasSpectrum usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A1 .""" ;
                rdfs:comment "It assigns a MS2 spectrum to, for instance, a LCMS feature set. The domain is not defined to provide flexibility. For a LCMS feature set prefer to state the  emi:hasLCMSFeature property." ;
                rdfs:label "has spectrum" .


###  https://w3id.org/emi#hasSuperClass
emi:hasSuperClass rdf:type owl:ObjectProperty ;
                  rdfs:subPropertyOf emi:isClassifiedWith ;
                  rdfs:domain [ rdf:type owl:Class ;
                                owl:unionOf ( emi:ChemicalStructure
                                              emi:ChemicalTaxonAnnotation
                                            )
                              ] ;
                  rdfs:range npc:Superclass ;
                  vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix npc: <https://w3id.org/emi/npc#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:hasSuperClass npc:SESQUITERPENOIDS .""" ;
                  rdfs:label "has super class" .


###  https://w3id.org/emi#hasSource
emi:hasSource rdf:type owl:ObjectProperty ;
               rdfs:domain emi:Interaction ;
               rdfs:range sosa:Sample ;
               rdfs:label "has source" ; 
               rdfs:comment "An interaction system has a source sample that interacts with a target one. emi:hasSource should state the origin of an interaction." .


###  https://w3id.org/emi#hasTarget
emi:hasTarget rdf:type owl:ObjectProperty ;
               rdfs:domain emi:Interaction ;
               rdfs:range sosa:Sample ;
               rdfs:label "has target"  ;
               rdfs:comment "An interaction system has a source sample that interacts with a target one. emi:hasTarget should state the target of an interaction." .


###  https://w3id.org/emi#has_habitat
emi:hasHabitat rdf:type owl:ObjectProperty ;
                rdfs:domain emi:Interaction ;
                rdfs:range emi:Habitat ;
                rdfs:comment "It can be used to assign a habitat to an interaction system such as from GloBI. When applicable, we recommend to state ENVO or CMECS vocabulary terms." ;
                rdfs:label "has habitat" .

###  https://w3id.org/emi#inTaxon
emi:inTaxon rdf:type owl:ObjectProperty ;
            rdfs:domain [ rdf:type owl:Class ;
                          owl:unionOf ( sosa:Sample
                                        emi:InChIKey
                                        emi:Organism
                                      )
                        ] ;
            rdfs:range [ rdf:type owl:Class ;
                         owl:unionOf ( up:Taxon
                                       emi:Taxon
                                     )
                       ] ;
            rdfs:label "found in taxon" .


###  https://w3id.org/emi#isClassifiedWith
emi:isClassifiedWith rdf:type owl:ObjectProperty ;
                     vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix npc: <https://w3id.org/emi/npc#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:isClassifiedWith npc:CADINANE_SESQUITERPENOIDS .""" ;
                     rdfs:comment "It is used to classify any individidual with an external controlled-vocabulary in case rdf:type is not the most suitable solution." ;
                     rdfs:label "is classified with" .


###  https://w3id.org/emi#isInChIKey2DOf
emi:isInChIKey2DOf rdf:type owl:ObjectProperty ,
                            owl:InverseFunctionalProperty ;
                   rdfs:domain emi:InChIKey2D ;
                   rdfs:range emi:InChIKey ;
                   vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix wd: <http://www.wikidata.org/entity/> .
:ZCCLDKGWJIREQF-PDBXOOCHSA-N rdf:type emi:InChIKey2D ;
            emi:isInChIKey2DOf :ZCCLDKGWJIREQF ;
            rdfs:label \"ZCCLDKGWJIREQF\" .
:ZCCLDKGWJIREQF-PDBXOOCHSA-N rdf:type emi:InChIKey. """ ;
                   rdfs:comment "It can be used to assign an InChIKey2D to an InChIKey that represents a chemical structure." ;
                   rdfs:label "is InChIKey2D of" .


###  https://w3id.org/emi#isInChIKeyOf
emi:isInChIKeyOf rdf:type owl:ObjectProperty ;
                 rdfs:domain emi:InChIKey ;
                 rdfs:range [ rdf:type owl:Class ;
                              owl:unionOf ( emi:Chemical
                                            emi:SpectrumAnnotation
                                          )
                            ] ;
                 vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix wd: <http://www.wikidata.org/entity/> .
@prefix dcterms: < http://purl.org/dc/terms/> .
wd:Q27145340 rdf:type emi:Chemical ;
             dcterms:identifier \"Q27145340\" .
 :ZCCLDKGWJIREQF-PDBXOOCHSA-N  emi:isInChIKeyOf wd:Q27145340 . """ ;
                 rdfs:label "is InChIKey of" .



#################################################################
#    Data properties
#################################################################



###  https://w3id.org/emi#componentLink
emi:componentLink rdf:type owl:DatatypeProperty ,
                           owl:FunctionalProperty ;
                  rdfs:domain emi:GNPSConsensusSpectrum ;
                  rdfs:range xsd:anyURI ;
                  rdfs:label "component link" .


###  https://w3id.org/emi#hasAdduct
emi:hasAdduct rdf:type owl:DatatypeProperty ;
              rdfs:domain emi:StructuralAnnotation ;
              rdfs:range xsd:string ;
              rdfs:label "has adduct" .


###  https://w3id.org/emi#hasClassProbability
emi:hasClassProbability rdf:type owl:DatatypeProperty ;
                        rdfs:subPropertyOf emi:hasProbability ;
                        rdfs:domain emi:ChemicalTaxonAnnotation ;
                        rdfs:range xsd:double ;
                        vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:hasClassProbability \"0.6451306343078613\"^^xsd:double .""" .


###  https://w3id.org/emi#hasConsistencyScore
emi:hasConsistencyScore rdf:type owl:DatatypeProperty ;
                        rdfs:subPropertyOf emi:hasScore ;
                        rdfs:domain emi:StructuralAnnotation ;
                        rdfs:range xsd:integer ;
                        rdfs:comment "An ISDB score." ;
                        rdfs:label "has consistency score" .


###  https://w3id.org/emi#hasCosine
emi:hasCosine rdf:type owl:DatatypeProperty ,
                       owl:FunctionalProperty ;
              rdfs:domain emi:SpectralPair ;
              rdfs:range xsd:double ;
              rdfs:label "has cosine" .


###  https://w3id.org/emi#hasCosmicScore
emi:hasCosmicScore rdf:type owl:DatatypeProperty ;
                   rdfs:subPropertyOf emi:hasScore ;
                   rdfs:domain emi:StructuralAnnotation ;
                   rdfs:range xsd:double ;
                   rdfs:label "has cosmic score" .


###  https://w3id.org/emi#hasFeatureArea
emi:hasFeatureArea rdf:type owl:DatatypeProperty ;
                   rdfs:range xsd:double ;
                   vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasFeatureArea \"1180836.665658199\"^^xsd:double .""" ;
                   rdfs:comment "Assign a feature area to a MS2 spectrum." ;
                   rdfs:label "has feature area" .


###  https://w3id.org/emi#hasFinalScore
emi:hasFinalScore rdf:type owl:DatatypeProperty ;
                  rdfs:subPropertyOf emi:hasScore ;
                  rdf:type owl:FunctionalProperty ;
                  rdfs:domain emi:StructuralAnnotation ;
                  rdfs:range xsd:double ;
                  rdfs:comment "An ISDB score." ;
                  rdfs:label "has final score" .


###  https://w3id.org/emi#hasGNPSLCMSLink
emi:hasGNPSLCMSLink rdf:type owl:DatatypeProperty ;
                    rdfs:domain emi:LCMSAnalysis ;
                    rdfs:range xsd:anyURI ;
                    vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
:VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysis ;
            emi:hasGNPSLCMSLink \"https://dashboard.gnps2.org/?usi=mzspec%3AMSV000087728%3AVGF138_A02_neg.mzXML\"^^xsd:anyURI .""" ;
                    rdfs:comment "It relates  GNPS LCMS link to a LCMS Analysis." ;
                    rdfs:label "has GNPS LCMS link" .


###  https://w3id.org/emi#hasIonization
emi:hasIonization rdf:type owl:DatatypeProperty ,
                           owl:FunctionalProperty ;
                  rdfs:domain <http://org.semanticweb.owlapi/error#Error1> .


###  https://w3id.org/emi#hasMassDifference
emi:hasMassDifference rdf:type owl:DatatypeProperty ,
                               owl:FunctionalProperty ;
                      rdfs:domain emi:SpectralPair ;
                      rdfs:range xsd:double ;
                      rdfs:label "has Mass difference" .


###  https://w3id.org/emi#hasParentMass
emi:hasParentMass rdf:type owl:DatatypeProperty ;
                  rdfs:domain emi:LCMSFeature ;
                  rdfs:range xsd:double ;
                  vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasParentMass \"833.447509765625\"^^xsd:double .""" ;
                  rdfs:comment "The parent mass of a LCMS feature." ;
                  rdfs:label "has parent mass" .


###  https://w3id.org/emi#hasPathwayProbability
emi:hasPathwayProbability rdf:type owl:DatatypeProperty ;
                          rdfs:subPropertyOf emi:hasProbability ;
                          rdfs:domain emi:ChemicalTaxonAnnotation ;
                          rdfs:range xsd:double ;
                          vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:hasPathwayProbability \"0.5601769685745239\"^^xsd:double .""" .


###  https://w3id.org/emi#hasProbability
emi:hasProbability rdf:type owl:DatatypeProperty ;
                   rdfs:range xsd:double ;
                   vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:hasProbability \"0.5601769685745239\"^^xsd:double .""" ;
                   rdfs:label "has probability" .


###  https://w3id.org/emi#hasRawSpectrum
emi:hasRawSpectrum rdf:type owl:DatatypeProperty ;
                   rdfs:domain emi:LCMSFeature ;
                   rdfs:range xsd:string ;
                   vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasRawSpectrum \"((58.7747, 0.034375), (107.3847, 0.0453125), (177.2855, 0.0375), (185.9186, 0.0375), (243.0295, 0.484375), (257.0457, 0.21875), (270.0167, 0.0765625), (271.0244, 0.4375), (285.0398, 0.359375), (300.028, 0.15625), (313.0341, 0.171875), (314.0425, 1.0), (315.0507, 0.640625), (551.4942, 0.0453125), (619.0516, 0.0375), (675.5888, 0.0421875))\" .""" ;
                   rdfs:comment "The raw spectrum of a LCMS individual MS2 spectrum. Its value is a tuple of binary tuples (see vann:example)." .


###  https://w3id.org/emi#hasRelativeFeatureArea
emi:hasRelativeFeatureArea rdf:type owl:DatatypeProperty ;
                           rdfs:domain emi:LCMSFeature ;
                           rdfs:range xsd:double ;
                           vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasRelativeFeatureArea \"0.0004294112935902454\"^^xsd:double .""" ;
                           rdfs:comment "The relative feature area of a LCMS individual MS2 spectrum." ;
                           rdfs:label "has relative feature area" .


###  https://w3id.org/emi#hasRetentionTime
emi:hasRetentionTime rdf:type owl:DatatypeProperty ;
                     rdfs:domain emi:LCMSFeature ;
                     rdfs:range xsd:double ;
                     vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasRetentionTime \"7.663716666666667\"^^xsd:double .""" ;
                     rdfs:comment "The retention time of a LCMS individual MS2 spectrum." ;
                     rdfs:label "has retention time" .


###  https://w3id.org/emi#hasRowId
emi:hasRowId rdf:type owl:DatatypeProperty ;
             rdfs:domain emi:LCMSFeature ;
             rdfs:range xsd:integer ;
             vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasRowId \"356\"^^xsd:integer .""" ;
             rdfs:comment "The row id of a LCMS individual MS2 spectrum." ;
             rdfs:label "has row id" .


###  https://w3id.org/emi#hasSMILES
emi:hasSMILES rdf:type owl:DatatypeProperty ,
                       owl:FunctionalProperty ;
              rdfs:domain emi:ChemicalStructure ;
              rdfs:range xsd:string ;
              rdfs:comment "The simplified molecular-input line-entry system (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings." ;
              rdfs:label "has SMILES" .


###  https://w3id.org/emi#hasScore
emi:hasScore rdf:type owl:DatatypeProperty ;
             rdfs:domain [ rdf:type owl:Class ;
                           owl:unionOf ( emi:Spec2VecDoc
                                         emi:StructuralAnnotation
                                       )
                         ] ;
             vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
:spec2vec_doc_mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:Spec2VecDoc ;
            emi:hasSpec2VecValue \"271.02\"^^xsd:double .""" ;
             rdfs:label "has score" .


###  https://w3id.org/emi#hasSpec2VecLoss
emi:hasSpec2VecLoss rdf:type owl:DatatypeProperty ;
                    rdfs:subPropertyOf emi:hasSpec2VecValue ;
                    rdfs:domain emi:Spec2VecDoc ;
                    rdfs:range xsd:double ;
                    vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
:spec2vec_doc_mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:Spec2VecDoc ;
            emi:hasSpec2VecLoss \"157.86\"^^xsd:double .""" ;
                    rdfs:comment "The Spec2Vec losses of a Spec2Vec document." ;
                    rdfs:label "has spec2vec loss" .


###  https://w3id.org/emi#hasSpec2VecPeak
emi:hasSpec2VecPeak rdf:type owl:DatatypeProperty ;
                    rdfs:subPropertyOf emi:hasSpec2VecValue ;
                    rdfs:domain emi:Spec2VecDoc ;
                    rdfs:range xsd:double ;
                    vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
:spec2vec_doc_mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:Spec2VecDoc ;
            emi:hasSpec2VecPeak \"271.02\"^^xsd:double .""" ;
                    rdfs:comment "The Spec2Vec peaks of a Spec2Vec document." ;
                    rdfs:label "has spec2vec peak" .


###  https://w3id.org/emi#hasSpec2VecValue
emi:hasSpec2VecValue rdf:type owl:DatatypeProperty ;
                     rdfs:subPropertyOf emi:hasScore ;
                     rdfs:domain emi:Spec2VecDoc ;
                     rdfs:range xsd:double ;
                     vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix : <https://w3id.org/emi/abox#> .
:spec2vec_doc_mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:Spec2VecDoc ;
            emi:hasSpec2VecValue \"271.02\"^^xsd:double .""" ;
                     rdfs:comment "A mass spectral similarity scoring through learning of structural relationships. Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data. Analysis and benchmarking of mass spectra similarity measures using gnps data set." ;
                     rdfs:label "has spec2vec value" .


###  https://w3id.org/emi#hasSpectralScore
emi:hasSpectralScore rdf:type owl:DatatypeProperty ;
                     rdfs:subPropertyOf emi:hasScore ;
                     rdf:type owl:FunctionalProperty ;
                     rdfs:domain emi:StructuralAnnotation ;
                     rdfs:range xsd:double ;
                     rdfs:comment "An ISDB score." ;
                     rdfs:label "has spectral score" .


###  https://w3id.org/emi#hasSuperClassProbability
emi:hasSuperClassProbability rdf:type owl:DatatypeProperty ;
                             rdfs:subPropertyOf emi:hasProbability ;
                             rdfs:domain emi:ChemicalTaxonAnnotation ;
                             rdfs:range xsd:double ;
                             vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation ;
            emi:hasSuperClassProbability \"0.34501510858535767\"^^xsd:double .""" .


###  https://w3id.org/emi#hasTaxoScore
emi:hasTaxoScore rdf:type owl:DatatypeProperty ;
                 rdfs:subPropertyOf emi:hasScore ;
                 rdf:type owl:FunctionalProperty ;
                 rdfs:domain emi:StructuralAnnotation ;
                 rdfs:range xsd:integer ;
                 rdfs:comment "An ISDB score." ;
                 rdfs:label "has taxo score" .


###  https://w3id.org/emi#hasUSI
emi:hasUSI rdf:type owl:DatatypeProperty ;
           rdfs:subPropertyOf owl:topDataProperty ;
           rdf:type owl:FunctionalProperty ;
           rdfs:domain [ rdf:type owl:Class ;
                         owl:unionOf ( emi:MS2Spectrum
                                       emi:StructuralAnnotation
                                     )
                       ] ;
           rdfs:range xsd:string ;
           vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature ;
            emi:hasUSI \"mzspec:MSV000087728:VGF153_A02_features_ms2_neg.mgf:scan:356\" .""" ;
           rdfs:comment "The universal spectrum identifier provided by GNPS." ;
           rdfs:label "has universal spectrum identifier" .


###  https://w3id.org/emi#hasZodiacScore
emi:hasZodiacScore rdf:type owl:DatatypeProperty ;
                   rdfs:subPropertyOf emi:hasScore ;
                   rdfs:domain emi:StructuralAnnotation ;
                   rdfs:range xsd:double ;
                   rdfs:label "has zodiac score" .


###  https://w3id.org/emi#inChIKey
emi:inChIKey rdf:type owl:DatatypeProperty ,
                      owl:FunctionalProperty ;
             rdfs:domain emi:InChIKey ;
             rdfs:range xsd:string ;
             rdfs:comment "The InChIKey data value, that is a textual representation of chemical structures. This value is composed of 27 characters and it is a condensed digital representation of the InChI." ;
             rdfs:label "InChIKey value" .


###  https://w3id.org/emi#inChIKey2D
emi:inChIKey2D rdf:type owl:DatatypeProperty ,
                        owl:FunctionalProperty ;
               rdfs:domain emi:InChIKey2D ;
               rdfs:range xsd:string ;
               rdfs:comment "The InChIKey 2D data value, that is a textual representation of chemical structures. This value is composed of the first 14 characters of its corresponding InChIKey of 27 character fixed length." ;
               rdfs:label "InChIKey 2D value" .


###  https://w3id.org/emi#scientificName
emi:scientificName rdf:type owl:DatatypeProperty ;
                   rdfs:domain emi:Taxon ;
                   rdfs:range xsd:string ;
                   rdfs:label "scientific name" .


###  https://w3id.org/emi#spectrumLink
emi:spectrumLink rdf:type owl:DatatypeProperty ,
                          owl:FunctionalProperty ;
                 rdfs:domain emi:GNPSConsensusSpectrum ;
                 rdfs:range xsd:anyURI ;
                 rdfs:label "spectrum link" .


#################################################################
#    Classes
#################################################################

###  http://org.semanticweb.owlapi/error#Error1
<http://org.semanticweb.owlapi/error#Error1> rdf:type owl:Class .


###  http://purl.uniprot.org/core/Rank
up:Rank rdf:type owl:Class ;
        rdfs:comment "A rank of a taxon." ;
        rdfs:isDefinedBy up: ;
        rdfs:label "Taxon rank" .


###  http://purl.uniprot.org/core/Taxon
up:Taxon rdf:type owl:Class ;
         rdfs:comment "An element of a taxonomy for classifying life forms." ;
         rdfs:isDefinedBy up: ;
         rdfs:label "Taxon" .


###  http://www.w3.org/ns/sosa/Observation
sosa:Observation vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix sosa: <http://www.w3.org/ns/sosa/> .
:VGF138_A02_neg.mzXML rdf:type sosa:Observation .""" .


###  http://www.wikidata.org/entity/Q16521
wd:Q16521 rdf:type owl:Class ;
          rdfs:subClassOf emi:Taxon ;
          rdfs:comment "An organism taxon in Wikidata." ;
          rdfs:label "Wikidata taxon" .


###  https://w3id.org/emi#Aliquot
emi:Aliquot rdf:type owl:Class ;
            rdfs:subClassOf sosa:Sample ;
            rdfs:comment "A sample taken from an extract sample for chemical analysis or other treatment." ;
            rdfs:label "Aliquot" .


###  https://w3id.org/emi#Analysis
emi:Analysis rdf:type owl:Class ;
             rdfs:subClassOf sosa:Observation ,
                             [ rdf:type owl:Restriction ;
                               owl:onProperty prov:used ;
                               owl:allValuesFrom prov:Entity
                             ] ,
                             [ rdf:type owl:Restriction ;
                               owl:onProperty prov:wasAssociatedWith ;
                               owl:allValuesFrom prov:Agent
                             ] ;
             vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:VGF138_A02_neg.mzXML rdf:type emi:Analysis .""" ;
             rdfs:comment "Any analysis performed over a sample." .


###  https://w3id.org/emi#AnatomicalEntity
emi:AnatomicalEntity rdf:type owl:Class ;
                     rdfs:comment "An anatomical entity can be an organism part (e.g. brain, blood, liver and so on) or a material anatomical entity such as a cell." ;
                     rdfs:label "Anatomical entity"@en ;
                     skos:closeMatch <http://purl.org/genex#AnatomicalEntity> .


###  https://w3id.org/emi#BioAssayResults
emi:BioAssayResults rdf:type owl:Class ;
                    rdfs:comment "An object to store bioactivity results." ;
                    rdfs:label "Bioassay result" .


###  https://w3id.org/emi#BioassayAnalysis
emi:BioassayAnalysis rdf:type owl:Class ;
                     rdfs:subClassOf emi:Analysis ;
                     rdfs:comment "A bioassay is an analytical method to determine the concentration or potency of a substance by its effect on living animals or plants (in vivo), or on living cells or tissues(in vitro)." ;
                     rdfs:isDefinedBy "https://en.wikipedia.org/wiki/Bioassay" ;
                     rdfs:label "Bioassay analysis" .


###  https://w3id.org/emi#Blank
emi:Blank rdf:type owl:Class ;
          rdfs:subClassOf sosa:Sample ;
          vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:VGF138_A12 rdf:type emi:Blank ;
            dcterms:identifier \"VGF138_A12\" .""" ;
          rdfs:comment "A blank sample." ;
          rdfs:label "Blank sample" .


###  https://w3id.org/emi#CSpair
emi:CSpair rdf:type owl:Class ;
           rdfs:subClassOf emi:SpectralPair ;
           rdfs:comment "A pair of 2 GNPSConsensusSpectra." ;
           rdfs:label "GNPS consensus spectra pair" .


###  https://w3id.org/emi#Chemical
emi:Chemical rdf:type owl:Class ;
             rdfs:subClassOf emi:ChemicalEntity ;
             vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix wd: <http://www.wikidata.org/entity/> .
@prefix dcterms: < http://purl.org/dc/terms/> .
wd:Q27145340 rdf:type emi:Chemical ;
            dcterms:identifier \"Q27145340\" ;
            emi:hasInChIKey :ZCCLDKGWJIREQF-PDBXOOCHSA-N ;
            rdfs:label \"ZCCLDKGWJIREQF-PDBXOOCHSA-N\" .""" ;
             rdfs:comment "A chemical. Recommendation: the instances of this class are ideally Wikidata chemical entries. If it is not a Wikidata entry we recommend to be as much as possible consistent in the whole dataset. Metadata can also be provided in order to describe the provenance of the instance (a chemical), for example, by stating the property prov-o:wasDerivedFrom (PROV-Ontology)." ;
             rdfs:label "Chemical" .


###  https://w3id.org/emi#ChemicalEntity
emi:ChemicalEntity rdf:type owl:Class ;
                   rdfs:comment "A chemical entity (chemical structure or class)." ;
                   rdfs:label "Chemical entity" .


###  https://w3id.org/emi#ChemicalStructure
emi:ChemicalStructure rdf:type owl:Class ;
                      rdfs:subClassOf emi:ChemicalEntity ;
                      rdfs:comment "A representation of one or more chemical structures. This representation can be defined as molecular information encodings, compact encoding representations, chemical formulas and graphical representations." ;
                      rdfs:label "Chemical structure representation" .


###  https://w3id.org/emi#ChemicalTaxon
emi:ChemicalTaxon rdf:type owl:Class ;
                  rdfs:subClassOf emi:ChemicalEntity ;
                  rdfs:comment "As a taxonomy for chemicals such as natural products, we recommend to use the taxonomy derived from NPClassifier (i.e., https://w3id.org/emi/npc)." ;
                  rdfs:label "Chemical taxon" .


###  https://w3id.org/emi#ChemicalTaxonAnnotation
emi:ChemicalTaxonAnnotation rdf:type owl:Class ;
                            rdfs:subClassOf emi:SpectrumAnnotation ;
                            owl:disjointWith emi:StructuralAnnotation ;
                            vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:ChemicalTaxonAnnotation .""" ;
                            rdfs:comment "This class is used to annotate a spectrum feature with a chemical taxon. Prefer the Chemical structure annotation class, if the annotation is mainly to assign a chemical representation structure as defined in the emi:ChemicalStructure." ;
                            rdfs:label "Chemical taxon annotation" .


###  https://w3id.org/emi#ComputationalAnalysis
emi:ComputationalAnalysis rdf:type owl:Class ;
                          rdfs:subClassOf emi:Analysis ;
                          rdfs:label "Computational analysis" ;
                          rdfs:comment "A data analysis made with computational resources (e.g., computers, software tools)." .


###  https://w3id.org/emi#ContinousTrait
emi:ContinousTrait rdf:type owl:Class ;
                   rdfs:subClassOf emi:Trait ;
                   rdfs:label "Continuous trait" ;
                   rdfs:comment "A specific quantitative characteristic of an individual such as height and blood pressure." . 

###  https://w3id.org/emi#Trait
emi:Trait   rdf:type owl:Class ;
            rdfs:subClassOf sosa:Result ;
            rdfs:label "Trait" ;
            rdfs:comment "A specific characteristic of an individual. Traits can be determined by genes, environmental factors or by a combination of both. Traits can be discrete (i.e., qualitative such as color) or continuous (quantitative such as height)." . 


###  https://w3id.org/emi#DevelopmentalStage
emi:DevelopmentalStage rdf:type owl:Class ;
                       rdfs:comment "A developmental stage is spatiotemporal region encompassing some part of the life cycle of an organism, e.g., blastula stage. We recommend to use the developmental stage terms from UBERON of a source or target organism sample in an interaction system such as from GloBI.";
                       rdfs:label "Developmental stage" ;
                       skos:closeMatch <http://www.ebi.ac.uk/efo/EFO_0000399> .


###  https://w3id.org/emi#DiscreteTrait
emi:DiscreteTrait rdf:type owl:Class ;
                  rdfs:subClassOf emi:Trait ;
                  rdfs:label "Discrete trait" ;
                  vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix qudt: <http://qudt.org/schema/qudt/> .
@prefix unit: <http://qudt.org/vocab/unit/> .
:flower-color rdf:value  red ;
              qudt:hasUnit unit:X .""" ;
              rdfs:comment "A discrete trait structured value. When applicable, value units should be defined as the QUDT Units Vocabulary terms." . 


###  https://w3id.org/emi#ExtractSample
emi:ExtractSample rdf:type owl:Class ;
                  rdfs:subClassOf sosa:Sample ;
                  rdfs:comment "A natural extract obtained from the processing of a RawMaterial." ;
                  rdfs:label "Extract sample" .


###  https://w3id.org/emi#FBMNComponent
emi:FBMNComponent rdf:type owl:Class ;
                  rdfs:comment "Feature-based molecular network component." ;
                  rdfs:label "FBMN component" .


###  https://w3id.org/emi#GNPSAnnotation
#emi:GNPSAnnotation rdf:type owl:Class ;
#                   rdfs:subClassOf emi:StructuralAnnotation ;
#                   rdfs:comment "A spectrum structural annotation by GNPS." ;
#                   rdfs:label "GNPS structural annotation" ;
#                   owl:deprecated "delete it, it is better to model the source separately becuase otherwise it would require to add a new class each time a new source of annotation appears. the only advantage of keeping the model like this is to reduce the number of triples." .


###  https://w3id.org/emi#GNPSConsensusSpectrum
emi:GNPSConsensusSpectrum rdf:type owl:Class ;
                          rdfs:subClassOf emi:MS2Spectrum ;
                          rdfs:comment "An MS2 spectrum corresponding to the GNPS consensus spectrum of 1 or more LCMSFeature. Recommendation: instances of this class are ideally built as follows: \"https://metabolomics-usi.ucsd.edu/dashinterface/?usi1={id}\", e.g.: \"https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=mzspec:MassIVE:TASK-773effaad17c4124b9ea9004eaa3f526-spectra/specs_ms.mgf:scan:1028\"." ;
                          rdfs:label "GNPS consensus MS2 spectrum" .


###  https://w3id.org/emi#BiologicalSex
emi:BiologicalSex rdf:type owl:Class ;
           rdfs:label "biological sex"@en ;
           rdfs:comment "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved [source: http://purl.obolibrary.org/obo/PATO_0000047]. We recommend to use PATO ontology terms for inviduals of this class." ; 
           skos:closeMatch <http://purl.obolibrary.org/obo/PATO_0000047> . 


###  https://w3id.org/emi#ISDBAnnotation
#emi:ISDBAnnotation rdf:type owl:Class ;
#                   rdfs:subClassOf emi:StructuralAnnotation ;
#                   rdfs:comment "A spectrum structural annotation by comparison with an in-silico spectral DB, coupled to chemical and taxonomical reweighting." ;
#                   rdfs:label "ISDB structural annotation" ;
#                   owl:deprecated "delete it, it is better to model the source separately becuase otherwise it would require to add a new class each time a new source of annotation appears. the only advantage of keeping the model like this is to reduce the number of triples." .


###  https://w3id.org/emi#InChIKey
emi:InChIKey rdf:type owl:Class ;
             rdfs:subClassOf emi:ChemicalStructure ,
                             [ rdf:type owl:Restriction ;
                               owl:onProperty emi:inChIKey ;
                               owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
                               owl:onDataRange xsd:string
                             ] ;
             rdfs:comment "A chemical structure represented by its InChIKey." ;
             rdfs:label "InChIKey" .


###  https://w3id.org/emi#InChIKey2D
emi:InChIKey2D rdf:type owl:Class ;
               rdfs:subClassOf emi:ChemicalStructure ,
                               [ rdf:type owl:Restriction ;
                                 owl:onProperty emi:isInChIKey2DOf ;
                                 owl:someValuesFrom emi:InChIKey
                               ] ,
                               [ rdf:type owl:Restriction ;
                                 owl:onProperty emi:inChIKey2D ;
                                 owl:qualifiedCardinality "1"^^xsd:nonNegativeInteger ;
                                 owl:onDataRange xsd:string
                               ] ;
               rdfs:comment "A collection of chemical structures that share the first 14 characters of their InChIKeys, often returned by mass spectrometry based annotation tools." ;
               rdfs:label "2D InChIKey" .


###  https://w3id.org/emi#InformationSource
emi:InformationSource rdf:type owl:Class ;
                      rdfs:comment "The source of information. For example, the source of a given annotation that might be a bioinformatics database or machine learning classification model." ;
                      rdfs:label "Information source" ;
                      skos:note """This can be replaced by or related with the provenance ontology (W3C recommendation).
https://www.w3.org/TR/prov-o/""" .


###  https://w3id.org/emi#Interaction
emi:Interaction rdf:type owl:Class ;
                rdfs:subClassOf prov:Activity ;
                rdfs:comment "An interaction record listed (e.g.,in GloBI database) between Source and Target samples." ;
                rdfs:label "Interaction System" .



###  https://w3id.org/emi#InteractionType
emi:InteractionType rdf:type owl:Class ;
                    rdfs:comment "It represents the kind of interaction between a source and a target organism sample in an interaction system (e.g., has pathogen and allelopath of). We recommed using RO vocabulary terms." ;
                    rdfs:label "Interaction type" ;
                    vann:example """@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:INTERACTION-1 a emi:Interaction ;
    emi:isClassifiedWith obo:RO_0002557 . #has pathogen
obo:RO_0002557 a emi:InteractionType .""".


###  https://w3id.org/emi#LCMSAnalysis
emi:LCMSAnalysis rdf:type owl:Class ;
                 rdfs:subClassOf emi:Analysis ;
                 vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysis .""" ;
                 rdfs:comment "A liquid chromatography–mass spectrometry (LCMS) analysis in a given ionization mode (pos or neg)." ;
                 rdfs:label "LCMS analysis" .


###  https://w3id.org/emi#LCMSAnalysisNeg
emi:LCMSAnalysisNeg rdf:type owl:Class ;
                    rdfs:subClassOf emi:LCMSAnalysis ;
                    vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysisNeg .""" ;
                    rdfs:comment "An LCMS analysis in negative ionization mode (pos or neg)." ;
                    rdfs:label "Negative LCMS analysis" ;
                    emi:hasIonization "negative" .


###  https://w3id.org/emi#LCMSAnalysisPos
emi:LCMSAnalysisPos rdf:type owl:Class ;
                    rdfs:subClassOf emi:LCMSAnalysis ;
                    vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:VGF138_A02_pos.mzXML rdf:type emi:LCMSAnalysisPos .""" ;
                    rdfs:comment "An LCMS analysis in positive ionization mode (positive or negative)." ;
                    rdfs:label "Positive LCMS analysis" ;
                    emi:hasIonization "positive" .


###  https://w3id.org/emi#LCMSFeature
emi:LCMSFeature rdf:type owl:Class ;
                rdfs:subClassOf emi:MS2Spectrum ;
                vann:example """@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:LCMSFeature .""" ;
                rdfs:comment "An LCMS feature from a processed LCMS analysis. Recommendation: instances of this class are ideally built as follows: \"https://metabolomics-usi.ucsd.edu/dashinterface/?usi1={id}\" (e.g., https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=mzspec:MSV000090090:DBGI_01_04_001_features_ms2_pos.mgf:scan:1)." ;
                rdfs:label "LCMS individual MS2 spectrum" .


###  https://w3id.org/emi#LCMSFeatureSet
emi:LCMSFeatureSet rdf:type owl:Class ;
                   vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:VGF153_A02_lcms_feature_list_neg rdf:type emi:LCMSFeatureSet .""" ;
                   rdfs:comment "A set of Liquid chromatography–mass spectrometry (LCMS) features obtained from the processing of a given LCMS analysis." ;
                   rdfs:label "LCMS feature set" .


###  https://w3id.org/emi#LFpair
emi:LFpair rdf:type owl:Class ;
           rdfs:subClassOf emi:SpectralPair ;
           rdfs:comment "A pair of LCMSFeature." ;
           rdfs:label "LCMS feature pair" .


###  https://w3id.org/emi#LabObject
#emi:LabObject rdf:type owl:Class ;
#              rdfs:comment "An object that correspond to a physical laboratory object" ;
#              rdfs:label "Laboratory object" ;
#              owl:deprecated "To remove, it was replaced with Sample from Sosa, because the Lab Objcts in the EMI model so far are only kind of samples. Hence, there is no need of generalizing to any lab object or making it specific to a \"lab\"." .


###  https://w3id.org/emi#Locality
emi:Locality rdf:type owl:Class .


###  https://w3id.org/emi#MS2Spectrum
emi:MS2Spectrum rdf:type owl:Class ;
                vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
@prefix usi: <https://metabolomics-usi.ucsd.edu/dashinterface/?usi1=> .
usi:mzspec%3AMSV000087728%3AVGF153_A02_features_ms2_neg.mgf%3Ascan%3A356 rdf:type emi:MS2Spectrum .""" ;
                rdfs:comment "A fragmentation mass spectrometry (or MS2) spectrum." ;
                rdfs:label "MS2 spectrum" .


###  https://w3id.org/emi#Habitat
emi:Habitat rdf:type owl:Class ;
            rdfs:comment "It defines an environment where an emi:Interaction occurs. If applicable, we recommend to use the habitat terms from ENVO or CMECS of an interaction system such as from GloBI." ;
            rdfs:label "Habitat" .

###  https://w3id.org/emi#NonTrait
emi:NonTrait rdf:type owl:Class ;
             rdfs:subClassOf sosa:Result ;
             vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:EXAMPLE-NON-TRAIT rdf:type emi:NonTrait ;
    rdf:value  12.4""" ;
              rdfs:comment "A non trait structured value. When applicable, value units should be defined as QUDT Units Vocabulary terms." . 


###  https://w3id.org/emi#Organism
emi:Organism rdf:type owl:Class ;
             rdfs:subClassOf emi:System ;
             rdfs:comment "A living being, such as an animal, a plant, a bacterium, or a fungus., Any individual living (or previously living) being. Example: animal, human being. An organism is associated to a taxon such as \"Homo Sapiens\", NCBI taxonomy identifier: 9606." ;
             rdfs:label "Organism" ;
             rdfs:seeAlso <http://purl.org/net/orth#Organism> ;
             skos:altLabel "Living being" .

###  https://w3id.org/emi#OrganismGroup
emi:OrganismGroup rdf:type owl:Class ;
             rdfs:comment "A group of organisms (see emi:Organism). These organims may be grouped by biological sex (emi:BiologicalSex), for example." ;
             rdfs:label "Group of organisms" ;
             skos:altLabel "Organism group", "Organism cluster", "Cluster of organisms" .


###  https://w3id.org/emi#PhysiologicalStage
emi:PhysiologicalStage rdf:type owl:Class ;
                       rdfs:label "Physiological stage" ;
                       rdfs:comment "A physiological stage is a specific phase or condition of an organism in its life cycle (e.g., viability stage). If applicable, we recommend to use the physiological stage terms from PATO of a source or target organism sample in an interaction system such as from GloBI." .


###  https://w3id.org/emi#QCSample
emi:QCSample rdf:type owl:Class ;
             rdfs:subClassOf sosa:Sample ;
             rdfs:comment "A quality control (QC) sample." ;
             rdfs:label "Quality control sample" .


###  https://w3id.org/emi#RawMaterial
emi:RawMaterial rdf:type owl:Class ;
                rdfs:subClassOf sosa:Sample ;
                rdfs:comment "A raw laboratory biological material, i.e., before extraction." ;
                rdfs:label "Raw material" .


###  https://w3id.org/emi#SIRIUSAnnotation
#emi:SIRIUSAnnotation rdf:type owl:Class ;
#                     rdfs:subClassOf emi:StructuralAnnotation ;
#                     rdfs:comment "A spectrum structural annotation by SIRIUS" ;
#                     rdfs:label "SIRIUS structural annotation" ;
#                     owl:deprecated "delete it, it is better to model the source separately becuase otherwise it would require to add a new class each time a new source of annotation appears. the only advantage of keeping the model like this is to reduce the number of triples." .


###  https://w3id.org/emi#SiriusCanopusAnnotation
#emi:SiriusCanopusAnnotation rdf:type owl:Class ;
#                            rdfs:subClassOf emi:ChemicalTaxonAnnotation ;
#                            rdfs:comment "A spectrum chemical class annotation by SIRIUS-CANOPUS." ;
#                            rdfs:label "CANOPUS chemical class annotation" ;
#                            owl:deprecated "to delete?" .


###  https://w3id.org/emi#Spec2VecDoc
emi:Spec2VecDoc rdf:type owl:Class ;
                rdfs:comment "Document about improved mass spectral similarity scoring through learning of structural relationships. Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data. Analysis and benchmarking of mass spectra similarity measures using GNPS data set." ;
                rdfs:label "Spec2vec document" .


###  https://w3id.org/emi#SpectralPair
emi:SpectralPair rdf:type owl:Class ;
                 rdfs:comment "A pair of two tandem mass spectrometry (MS2 spectra)." ;
                 rdfs:label "MS2Spectra pair" .


###  https://w3id.org/emi#SpectrumAnnotation
emi:SpectrumAnnotation rdf:type owl:Class ;
                       rdfs:subClassOf [ rdf:type owl:Restriction ;
                                         owl:onProperty prov:wasDerivedFrom ;
                                         owl:allValuesFrom emi:InformationSource
                                       ] ,
                                       [ rdf:type owl:Restriction ;
                                         owl:onProperty prov:wasGeneratedBy ;
                                         owl:allValuesFrom emi:Analysis
                                       ] ;
                       vann:example """@prefix : <https://w3id.org/emi/abox#> .
@prefix emi: <https://w3id.org/emi#> .
:CANOPUS-mzspec%3AMSV000087728%3AVGF147_E06_features_ms2_neg.mgf%3Ascan%3A45 rdf:type emi:SpectrumAnnotation .""" ;
                       rdfs:comment "A spectral annotation." ;
                       rdfs:label "Spectrum annotation" .


###  https://w3id.org/emi#StructuralAnnotation
emi:StructuralAnnotation rdf:type owl:Class ;
                         rdfs:subClassOf emi:SpectrumAnnotation ,
                                         [ rdf:type owl:Restriction ;
                                           owl:onProperty emi:hasChemicalStructure ;
                                           owl:someValuesFrom emi:InChIKey2D
                                         ] ;
                         rdfs:comment "This class is used to annotate a spectrum feature with a chemical representation structure as defined in the emi:ChemicalStructure. Prefer the  Chemical taxon annotation class, if the annotation is mainly to assign taxa to a spectrum feature." ;
                         rdfs:label "Chemical structure annotation" .


###  https://w3id.org/emi#System
emi:System rdf:type owl:Class ;
           rdfs:comment "Any part of the observable universe. A system is often composed of subsystems, for example, the Earth system contains a biome that contains a population that contains organisms that contains organs and so on." ;
           rdfs:label "System" .


###  https://w3id.org/emi#Taxon
emi:Taxon rdf:type owl:Class ;
          rdfs:comment "Organism taxon. In the context of open research data, we recommend the use of Wikidata taxonomy as the classification and nomenclature for all of the organisms." ;
          rdfs:label "Organism taxon" .


###  https://w3id.org/emi#WDChemical
#emi:WDChemical rdf:type owl:Class ;
#               rdfs:subClassOf emi:XRef ;
#               rdfs:comment "Cross-reference to a chemical entity in Wikidata." ;
#               rdfs:label "Cross-reference to a chemical entity in Wikidata" ;
#               owl:deprecated "delete?" .


###  https://w3id.org/emi#WDChemicalStructure
emi:WDChemicalStructure rdf:type owl:Class ;
                        rdfs:subClassOf emi:Chemical ;
                        rdfs:comment "A Wikidata chemical entry." ;
                        rdfs:label "Wikidata chemical" .


###  https://w3id.org/emi#XRef
#emi:XRef rdf:type owl:Class ;
#         rdfs:comment "Any cross-reference." ;
#         rdfs:label "Any cross-reference" ;
#         owl:deprecated "delete?" .


###  https://w3id.org/emi/npc#Class
npc:Class rdf:type owl:Class ;
          rdfs:subClassOf skos:Concept ,
                          emi:ChemicalTaxon ,
                          [ rdf:type owl:Restriction ;
                            owl:onProperty skos:broader ;
                            owl:someValuesFrom npc:Superclass
                          ] ;
          owl:disjointWith [ rdf:type owl:Class ;
                             owl:unionOf ( npc:Pathway
                                           npc:Superclass
                                         )
                           ] ;
          rdfs:comment "The Superclasses are subdivided into Classes that represent specific compound families (e.g., erythromycins, penicillins, or cannabinoids), characteristic functional groups (e.g., chromones, azaphilones, indole alkaloids, or 3-spiro tetramic acids), or scaffold diversity within a Superclass (e.g., flavans, flavones, and chalcones from flavonoids)." ;
          rdfs:label "Natural product class" .


###  https://w3id.org/emi/npc#Pathway
npc:Pathway rdf:type owl:Class ;
            rdfs:subClassOf skos:Concept ,
                            emi:ChemicalTaxon ;
            owl:disjointWith [ rdf:type owl:Class ;
                               owl:unionOf ( npc:Class
                                             npc:Superclass
                                           )
                             ] ;
            rdfs:comment "The highest level of a hierarchical chemical structure classification such as those defined with the NPClassifier, a deep-learning tool for the automated structural classification of natural products (NP) from their counted Morgan fingerprints. The Pathways of NPClassifier consist of seven categories: fatty acids, polyketides, shikimates–phenylpropanoids, terpenoids, alkaloids, amino acids/peptides, and carbohydrates." ;
            rdfs:label "Natural product pathway" .


###  https://w3id.org/emi/npc#Superclass
npc:Superclass rdf:type owl:Class ;
               rdfs:subClassOf skos:Concept ,
                               emi:ChemicalTaxon ,
                               [ rdf:type owl:Restriction ;
                                 owl:onProperty skos:broader ;
                                 owl:someValuesFrom npc:Pathway
                               ] ;
               owl:disjointWith [ rdf:type owl:Class ;
                                  owl:unionOf ( npc:Class
                                                npc:Pathway
                                              )
                                ] ;
               rdfs:comment "The Superclasses represent subcategories within the Pathways. The categories in the Superclass originate from the general classes of metabolites (e.g., flavonoids, meroterpenoids, or steroids), the general chemical or molecular shapes (e.g., chromanes, phloroglucinols, or macrolides), or biosynthetic information (e.g., tryptophan alkaloids, aromatic polyketides, or pseudo alkaloids)." ;
               rdfs:label "Natural product superclass" .



#################################################################
#    Individuals
#################################################################

###  https://www.sib.swiss
<https://www.sib.swiss> rdf:type owl:NamedIndividual ,
                                 foaf:Organization ;
                        foaf:homepage <https://www.sib.swiss> ;
                        foaf:name "SIB Swiss Institute of Bioinformatics"@en .


###  https://www.unifr.ch
<https://www.unifr.ch> rdf:type owl:NamedIndividual ,
                                foaf:Organization ;
                       foaf:homepage <https://www.unifr.ch> ;
                       foaf:name "University of Fribourg"@en .


###  https://www.unige.ch
<https://www.unige.ch> rdf:type owl:NamedIndividual ,
                                foaf:Organization ;
                       foaf:homepage <https://www.unige.ch> ;
                       foaf:name "University of Geneva"@en .

###  https://www.unine.ch
<https://www.unine.ch> rdf:type owl:NamedIndividual ,
                                foaf:Organization ;
                       foaf:homepage <https://www.unine.ch> ;
                       foaf:name "University of Neuchâtel"@en .

<https://orcid.org/0000-0002-3175-5372> a foaf:Person ;
    foaf:name "Tarcisio Mendes de Farias"@en ;
    org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0000-0001-9292-9463> a foaf:Person ;
foaf:name "Marco Pagni"@en ;
  org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0000-0002-3648-7362> a foaf:Person ;
foaf:name "Arnaud Gaudry"@en ;
  org:memberOf <https://www.unige.ch> .
<https://orcid.org/0000-0002-9619-1707> a foaf:Person ;
foaf:name "Florence Mehl"@en ;
  org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0000-0003-3389-2191> a foaf:Person ;
foaf:name "Pierre-Marie Allard"@en ;
  org:memberOf <https://www.unifr.ch> .
<https://orcid.org/0000-0002-1269-2038> a foaf:Person ;
foaf:name "Luca Cappelletti"@en ;
  org:memberOf <https://www.unifr.ch> .
<https://orcid.org/0000-0003-3213-4495> a foaf:Person ;
foaf:name "Ana Claudia Sima"@en ;
  org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0009-0005-5515-1230> a foaf:Person ;
foaf:name "Disha Tandon"@en ;
  org:memberOf <https://www.unine.ch> .

###  Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi