The Earth Metabolome Initiative (EMI) ontology
type: Ontology
version IRI: https://w3id.org/emi/version/1.0
imports: core
imports: prov-o-20130430
imports: sosa
imports: npc
imports: terms
imports: wgs84 pos#
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).
bibliographic citation: The Earth Metabolome Initiative Consortium. The Earth Metabolome Initiative (EMI) ontology. Revision: 1.0. Retrieved from: https://w3id.org/emi/version/1.0
contributor: Marco Pagni
contributor: Arnaud Gaudry
contributor: Florence Mehl
contributor: Pierre-Marie Allard
contributor: Luca Cappelletti
contributor: Tarcisio Mendes de Farias
contributor: Ana Claudia Sima
contributor: Disha Tandon
created: 2023-11-02
creator: Tarcisio Mendes de Farias
description: The Earth Metabolome Initiative (EMI) ontology is designed to capture and structure the metabolic content of all currently known species on our planet.
issue: 2024-04-03
license: https://creativecommons.org/publicdomain/zero/1.0
modified: 2025-07-15
publisher: www.earthmetabolome.org
Replaces: https://purl.org/emi/version/0.3
status: draft
preferred namespace prefix: emi
preferred namespace uri: https://w3id.org/emi#
code repository: https://github.com/earth-metabolome-initiative/earth_metabolome_ontology
version info: 1.0
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…

Replaces
type: AnnotationProperty
description: This property is intended to be used with non-literal values. This property is an inverse property of Is Replaced By.
issued: 2000-07-11
comment: A related resource that is supplanted, displaced, or superseded by the described resource.

alternative label
type: AnnotationProperty
comment: The range of skos:altLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: An alternative lexical label for a resource.
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).
sub property of: label

preferred label
type: AnnotationProperty
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.
comment: The range of skos:prefLabel is the class of RDF plain literals.
comment: skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties.
definition: The preferred lexical label for a resource, in a given language.
sub property of: label

rank
type: ObjectProperty
domain: Taxon
range: Taxon rank
comment: The rank of a taxon.

hasResult
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.

has anatomical entity
type: ObjectProperty
domain: Sample
range: Anatomical entity
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.

has annotation
type: ObjectProperty
domain: MS2 spectrum
range: Spectrum annotation

has chemical structure representation
type: ObjectProperty
domain: Chemical structure annotation
range: Chemical structure representation
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.

has class
type: ObjectProperty
sub property of: is classified with
domain: Class
  union of: Chemical structure representation
  union of: Chemical taxon annotation
range: Natural product class
property disjoint with: has super class
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" .

has consensus spectrum
type: ObjectProperty
sub property of: has spectrum
type: FunctionalProperty
domain: LCMS individual MS2 spectrum
range: GNPS consensus MS2 spectrum

has developmental stage
type: ObjectProperty
domain: Sample
range: Developmental stage
comment: The source or target organism sample of an interaction system such as GloBI can have a developmental stage.

has FBMN component
type: ObjectProperty
domain: LCMS individual MS2 spectrum
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 .
comment: Feature-based molecular network component.

has first member
type: ObjectProperty
sub property of: has pair member
type: FunctionalProperty
domain: LCMS feature pair
range: LCMS individual MS2 spectrum
comment: The first member of a spectral pair.

has InChIKey
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is InChIKey of
domain: Class
  union of: Chemical
  union of: Spectrum annotation
range: InChIKey
property chain axiom: has chemical structure representation
property chain axiom: is InChIKey2D of
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 .
comment: It can be used to assign an InChIKey either to a chemical or to an spectrum annotation.

has InChIKey2D
type: ObjectProperty
sub property of: topObjectProperty
inverse of: is InChIKey2D of
type: FunctionalProperty
domain: InChIKey
range: 2D InChIKey
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 .
comment: It can be used to represent the InChIKey2D of an emi:InChIKey that is chemical structure.

has LCMS feature
type: ObjectProperty
sub property of: has spectrum
domain: LCMS feature set
range: LCMS individual MS2 spectrum
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 .
comment: It relates a LCMS feature set to a feature.

has LCMS feature set
type: ObjectProperty
sub property of: hasResult
domain: LCMS analysis
range: LCMS feature set
example: @prefix emi: <https://w3id.org/emi#> . :VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysis ; emi:hasLCMSFeatureSet :VGF153_A02_lcms_feature_list_neg .
comment: It relates a LCMS analysis to a set of features.

has Massive DOI.
type: ObjectProperty
domain: LCMS analysis
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> .
comment: It assigns a Massive repository DOI to a LCMS Analysis.

has pair member
type: ObjectProperty
domain: MS2Spectra pair
range: MS2 spectrum
comment: LCMSFeature

has pathway
type: ObjectProperty
sub property of: is classified with
domain: Class
  union of: Chemical structure representation
  union of: Chemical taxon annotation
range: Natural product pathway
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 .

has physiological stage
type: ObjectProperty
domain: Sample
range: Physiological stage
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.

has second member
type: ObjectProperty
sub property of: has pair member
type: FunctionalProperty
domain: LCMS feature pair
range: LCMS individual MS2 spectrum
comment: The second member of a spectral pair.

has sex
type: ObjectProperty
domain: Class
  union of: Organism
  union of: Group of organisms
range: biological sex
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.

has spec2vec documentation
type: ObjectProperty
sub property of: topObjectProperty
domain: LCMS individual MS2 spectrum
range: Spec2vec document
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 .

has spectrum
type: ObjectProperty
range: MS2 spectrum
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 .
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.

has super class
type: ObjectProperty
sub property of: is classified with
domain: Class
  union of: Chemical structure representation
  union of: Chemical taxon annotation
range: Natural product superclass
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 .

has source
type: ObjectProperty
domain: Interaction System
range: Sample
comment: An interaction system has a source sample that interacts with a target one. emi:hasSource should state the origin of an interaction.

has target
type: ObjectProperty
domain: Interaction System
range: Sample
comment: An interaction system has a source sample that interacts with a target one. emi:hasTarget should state the target of an interaction.

has habitat
type: ObjectProperty
domain: Interaction System
range: Habitat
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.

found in taxon
type: ObjectProperty
domain: Class
  union of: Sample
  union of: InChIKey
  union of: Organism
range: Class
  union of: Taxon
  union of: Organism taxon

is classified with
type: ObjectProperty
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 .
comment: It is used to classify any individidual with an external controlled-vocabulary in case rdf:type is not the most suitable solution.

is InChIKey2D of
type: ObjectProperty
type: InverseFunctionalProperty
domain: 2D InChIKey
range: InChIKey
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.
comment: It can be used to assign an InChIKey2D to an InChIKey that represents a chemical structure.

is InChIKey of
type: ObjectProperty
domain: InChIKey
range: Class
  union of: Chemical
  union of: Spectrum annotation
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 .

component link
type: DatatypeProperty
type: FunctionalProperty
domain: GNPS consensus MS2 spectrum
range: anyURI

has adduct
type: DatatypeProperty
domain: Chemical structure annotation
range: string

hasClassProbability
type: DatatypeProperty
sub property of: has probability
domain: Chemical taxon annotation
range: double
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 .

has consistency score
type: DatatypeProperty
sub property of: has score
domain: Chemical structure annotation
range: integer
comment: An ISDB score.

has cosine
type: DatatypeProperty
type: FunctionalProperty
domain: MS2Spectra pair
range: double

has cosmic score
type: DatatypeProperty
sub property of: has score
domain: Chemical structure annotation
range: double

has feature area
type: DatatypeProperty
range: double
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 .
comment: Assign a feature area to a MS2 spectrum.

has final score
type: DatatypeProperty
sub property of: has score
type: FunctionalProperty
domain: Chemical structure annotation
range: double
comment: An ISDB score.

has GNPS LCMS link
type: DatatypeProperty
domain: LCMS analysis
range: anyURI
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 .
comment: It relates GNPS LCMS link to a LCMS Analysis.

has Mass difference
type: DatatypeProperty
type: FunctionalProperty
domain: MS2Spectra pair
range: double

has parent mass
type: DatatypeProperty
domain: LCMS individual MS2 spectrum
range: double
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 .
comment: The parent mass of a LCMS feature.

hasPathwayProbability
type: DatatypeProperty
sub property of: has probability
domain: Chemical taxon annotation
range: double
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 .

has probability
type: DatatypeProperty
range: double
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 .

hasRawSpectrum
type: DatatypeProperty
domain: LCMS individual MS2 spectrum
range: string
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))" .
comment: The raw spectrum of a LCMS individual MS2 spectrum. Its value is a tuple of binary tuples (see vann:example).

has relative feature area
type: DatatypeProperty
domain: LCMS individual MS2 spectrum
range: double
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 .
comment: The relative feature area of a LCMS individual MS2 spectrum.

has retention time
type: DatatypeProperty
domain: LCMS individual MS2 spectrum
range: double
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 .
comment: The retention time of a LCMS individual MS2 spectrum.

has row id
type: DatatypeProperty
domain: LCMS individual MS2 spectrum
range: integer
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 .
comment: The row id of a LCMS individual MS2 spectrum.

has SMILES
type: DatatypeProperty
type: FunctionalProperty
domain: Chemical structure representation
range: string
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.

has score
type: DatatypeProperty
domain: Class
  union of: Spec2vec document
  union of: Chemical structure annotation
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 .

has spec2vec loss
type: DatatypeProperty
sub property of: has spec2vec value
domain: Spec2vec document
range: double
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 .
comment: The Spec2Vec losses of a Spec2Vec document.

has spec2vec peak
type: DatatypeProperty
sub property of: has spec2vec value
domain: Spec2vec document
range: double
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 .
comment: The Spec2Vec peaks of a Spec2Vec document.

has spec2vec value
type: DatatypeProperty
sub property of: has score
domain: Spec2vec document
range: double
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 .
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.

has spectral score
type: DatatypeProperty
sub property of: has score
type: FunctionalProperty
domain: Chemical structure annotation
range: double
comment: An ISDB score.

hasSuperClassProbability
type: DatatypeProperty
sub property of: has probability
domain: Chemical taxon annotation
range: double
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 .

has taxo score
type: DatatypeProperty
sub property of: has score
type: FunctionalProperty
domain: Chemical structure annotation
range: integer
comment: An ISDB score.

has universal spectrum identifier
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: Class
  union of: MS2 spectrum
  union of: Chemical structure annotation
range: string
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" .
comment: The universal spectrum identifier provided by GNPS.

has zodiac score
type: DatatypeProperty
sub property of: has score
domain: Chemical structure annotation
range: double

InChIKey value
type: DatatypeProperty
type: FunctionalProperty
domain: InChIKey
range: string
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.

InChIKey 2D value
type: DatatypeProperty
type: FunctionalProperty
domain: 2D InChIKey
range: string
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.

scientific name
type: DatatypeProperty
domain: Organism taxon
range: string

spectrum link
type: DatatypeProperty
type: FunctionalProperty
domain: GNPS consensus MS2 spectrum
range: anyURI

Taxon rank
type: Class
comment: A rank of a taxon.

Taxon
type: Class
comment: An element of a taxonomy for classifying life forms.

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

Wikidata taxon
type: Class
subclass of: Organism taxon
comment: An organism taxon in Wikidata.

Aliquot
type: Class
subclass of: Sample
comment: A sample taken from an extract sample for chemical analysis or other treatment.

Analysis
type: Class
subclass of: Observation
subclass of: Restriction
  on property: used
  all values from: Entity
subclass of: Restriction
  on property: wasAssociatedWith
  all values from: Agent
example: @prefix : <https://w3id.org/emi/abox#> . @prefix emi: <https://w3id.org/emi#> . :VGF138_A02_neg.mzXML rdf:type emi:Analysis .
comment: Any analysis performed over a sample.

Anatomical entity
type: Class
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.

Bioassay result
type: Class
comment: An object to store bioactivity results.

Bioassay analysis
type: Class
subclass of: Analysis
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).

Blank sample
type: Class
subclass of: Sample
example: @prefix : <https://w3id.org/emi/abox#> . @prefix emi: <https://w3id.org/emi#> . :VGF138_A12 rdf:type emi:Blank ; dcterms:identifier "VGF138_A12" .
comment: A blank sample.

GNPS consensus spectra pair
type: Class
subclass of: MS2Spectra pair
comment: A pair of 2 GNPSConsensusSpectra.

Chemical
type: Class
subclass of: Chemical entity
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" .
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).

Chemical entity
type: Class
comment: A chemical entity (chemical structure or class).

Chemical structure representation
type: Class
subclass of: Chemical entity
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.

Chemical taxon
type: Class
subclass of: Chemical entity
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).

Chemical taxon annotation
type: Class
subclass of: Spectrum annotation
disjoint with: Chemical structure annotation
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 .
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.

Computational analysis
type: Class
subclass of: Analysis
comment: A data analysis made with computational resources (e.g., computers, software tools).

Continuous trait
type: Class
subclass of: Trait
comment: A specific quantitative characteristic of an individual such as height and blood pressure.

Trait
type: Class
subclass of: Result
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).

Developmental stage
type: Class
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.

Discrete trait
type: Class
subclass of: Trait
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 .
comment: A discrete trait structured value. When applicable, value units should be defined as the QUDT Units Vocabulary terms.

Extract sample
type: Class
subclass of: Sample
comment: A natural extract obtained from the processing of a RawMaterial.

FBMN component
type: Class
comment: Feature-based molecular network component.

GNPS consensus MS2 spectrum
type: Class
subclass of: MS2 spectrum
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".

biological sex
type: Class
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.

InChIKey
type: Class
subclass of: Chemical structure representation
subclass of: Restriction
  on property: InChIKey value
  qualified cardinality: 1
  on data range: string
comment: A chemical structure represented by its InChIKey.

2D InChIKey
type: Class
subclass of: Chemical structure representation
subclass of: Restriction
  on property: is InChIKey2D of
  some values from: InChIKey
subclass of: Restriction
  on property: InChIKey 2D value
  qualified cardinality: 1
  on data range: string
comment: A collection of chemical structures that share the first 14 characters of their InChIKeys, often returned by mass spectrometry based annotation tools.

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

Interaction System
type: Class
subclass of: Activity
comment: An interaction record listed (e.g.,in GloBI database) between Source and Target samples.

Interaction type
type: Class
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.
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 .

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

Negative LCMS analysis
type: Class
subclass of: LCMS analysis
example: @prefix : <https://w3id.org/emi/abox#> . @prefix emi: <https://w3id.org/emi#> . :VGF138_A02_neg.mzXML rdf:type emi:LCMSAnalysisNeg .
comment: An LCMS analysis in negative ionization mode (pos or neg).
has ionization: negative

Positive LCMS analysis
type: Class
subclass of: LCMS analysis
example: @prefix : <https://w3id.org/emi/abox#> . @prefix emi: <https://w3id.org/emi#> . :VGF138_A02_pos.mzXML rdf:type emi:LCMSAnalysisPos .
comment: An LCMS analysis in positive ionization mode (positive or negative).
has ionization: positive

LCMS individual MS2 spectrum
type: Class
subclass of: MS2 spectrum
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 .
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).

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

LCMS feature pair
type: Class
subclass of: MS2Spectra pair
comment: A pair of LCMSFeature.

MS2 spectrum
type: Class
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 .
comment: A fragmentation mass spectrometry (or MS2) spectrum.

Habitat
type: Class
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.

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

Organism
type: Class
subclass of: System
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.
alternative label: Living being

Group of organisms
type: Class
comment: A group of organisms (see emi:Organism). These organims may be grouped by biological sex (emi:BiologicalSex), for example.
alternative label: Organism group
alternative label: Organism cluster
alternative label: Cluster of organisms

Physiological stage
type: Class
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.

Quality control sample
type: Class
subclass of: Sample
comment: A quality control (QC) sample.

Raw material
type: Class
subclass of: Sample
comment: A raw laboratory biological material, i.e., before extraction.

Spec2vec document
type: Class
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.

MS2Spectra pair
type: Class
comment: A pair of two tandem mass spectrometry (MS2 spectra).

Spectrum annotation
type: Class
subclass of: Restriction
  on property: wasDerivedFrom
  all values from: Information source
subclass of: Restriction
  on property: wasGeneratedBy
  all values from: Analysis
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 .
comment: A spectral annotation.

Chemical structure annotation
type: Class
subclass of: Spectrum annotation
subclass of: Restriction
  on property: has chemical structure representation
  some values from: 2D InChIKey
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.

System
type: Class
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.

Organism taxon
type: Class
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.

Wikidata chemical
type: Class
subclass of: Chemical
comment: A Wikidata chemical entry.

Natural product class
type: Class
subclass of: Concept
subclass of: Chemical taxon
subclass of: Restriction
  on property: broader
  some values from: Natural product superclass
disjoint with: Class
  union of: Natural product pathway
  union of: Natural product superclass
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).

Natural product pathway
type: Class
subclass of: Concept
subclass of: Chemical taxon
disjoint with: Class
  union of: Natural product class
  union of: Natural product superclass
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.

Natural product superclass
type: Class
subclass of: Concept
subclass of: Chemical taxon
subclass of: Restriction
  on property: broader
  some values from: Natural product pathway
disjoint with: Class
  union of: Natural product class
  union of: Natural product pathway
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).

SIB Swiss Institute of Bioinformatics
type: NamedIndividual
type: Organization

University of Fribourg
type: NamedIndividual
type: Organization

University of Geneva
type: NamedIndividual
type: Organization

University of Neuchâtel
type: NamedIndividual
type: Organization

Tarcisio Mendes de Farias
type: Person
member of: SIB Swiss Institute of Bioinformatics

Marco Pagni
type: Person
member of: SIB Swiss Institute of Bioinformatics

Arnaud Gaudry
type: Person
member of: University of Geneva

Florence Mehl
type: Person
member of: SIB Swiss Institute of Bioinformatics

Pierre-Marie Allard
type: Person
member of: University of Fribourg

Luca Cappelletti
type: Person
member of: University of Fribourg

Ana Claudia Sima
type: Person
member of: SIB Swiss Institute of Bioinformatics

Disha Tandon
type: Person
member of: University of Neuchâtel