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The ENPKG RDF vocabulary

This version:
https://enpkg.commons-lab.org/kg/ontology_version/0.1.0
Revision:
0.1.0
Authors:
http://orcid.org/0000-0002-3648-7362
Contributors:
http://orcid.org/0000-0001-9292-9463
http://orcid.org/0000-0002-9619-1707
http://orcid.org/0000-0003-3389-2191
License:
https://creativecommons.org/licenses/by-nc-sa/4.0/
Visualization:
Visualize with WebVowl
Cite as:
http://orcid.org/0000-0002-3648-7362. The ENPKG RDF vocabulary. Revision: 0.1.0. Retrieved from: https://enpkg.commons-lab.org/kg/ontology_version/0.1.0
Provenance of this page
Ontology Specification Draft

Abstract

The RDF vocabulary describing concepts defined in the ENPKG dataset

Introduction back to ToC

This is a place holder text for the introduction. The introduction should briefly describe the ontology, its motivation, state of the art and goals.

Namespace declarations

Table 1: Namespaces used in the document
enpkg<https://enpkg.commons-lab.org/kg/>
void<http://rdfs.org/ns/void>
owl<http://www.w3.org/2002/07/owl>
xsd<http://www.w3.org/2001/XMLSchema>
skos<http://www.w3.org/2004/02/skos/core>
rdfs<http://www.w3.org/2000/01/rdf-schema>
orcid<http://orcid.org>
wd<http://www.wikidata.org/entity>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns>
xml<http://www.w3.org/XML/1998/namespace>
dcterms<http://purl.org/dc/terms>
vann<http://purl.org/vocab/vann>
foaf<http://xmlns.com/foaf/0.1>
sdo<http://schema.org>

The ENPKG RDF vocabulary: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Named Individuals

The ENPKG RDF vocabulary: Description back to ToC

This is a placeholder text for the description of your ontology. The description should include an explanation and a diagram explaining how the classes are related, examples of usage, etc.

Cross-reference for The ENPKG RDF vocabulary classes, object properties and data properties back to ToC

This section provides details for each class and property defined by The ENPKG RDF vocabulary.

Classes

2D InChIKeyc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/InChIkey2D

The first 14 characters of an InChIKey, often returned by MS-based annotation tools

A bioassay resultc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/BioAssayResults

An object to store bioactivity results

A chemical entity (chemical structure or class)c back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/ChemicalEntity

has sub-classes
InChIKey c, NPCClass c, NPCPathway c, NPCSuperclass c

A LabBlankc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LabBlank

A blank sample
has super-classes
A LabObject c

A LabExtractc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LabExtract

A natural extract obtained from the processing of a RawMaterial
has super-classes
A LabObject c

A LabObjectc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LabObject

An object that correspond to a physical laboratory object
has sub-classes
A LabBlank c, A LabExtract c, A LabQc c, A RawMaterial c

A LabQcc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LabQc

A quality control (QC) sample
has super-classes
A LabObject c

A RawMaterialc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/RawMaterial

A raw laboratory biological material, i.e. before extraction
has super-classes
A LabObject c

Any cross-referencec back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/XRef

Any cross-reference
has sub-classes
Cross-reference to a chemical entity in Wikidata c, Cross-reference to a taxon in Wikidata c

CANOPUS chemical class annotationc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/SiriusCanopusAnnotation

A spectrum chemical class annotation by SIRIUS-CANOPUS
has super-classes
Spectrum annotation c

Cross-reference to a chemical entity in Wikidatac back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/WDChemical

Cross-reference to a chemical entity in Wikidata
has super-classes
Any cross-reference c

Cross-reference to a taxon in Wikidatac back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/WDTaxon

Cross-reference to a taxon in Wikidata
has super-classes
Any cross-reference c

Feature listc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LCMSFeatureList

A list of LCMS features obtained from the processing of a given LCMS analysis

GNPS consensus MS2 spectrumc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/GNPSConsensusSpectrum

An MS2 spectrum corresponding to the GNPS consensus spectrum of 1 or more LCMSFeature
has super-classes
MS2 spectrum c
is in range of
member of a specral pair op

GNPS structural annotationc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/GNPSAnnotation

A spectrum structural annotation by GNPS
has super-classes
Spectrum annotation c

InChIKeyc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/InChIkey

A chemical structure represented by its InChIKey
has super-classes
A chemical entity (chemical structure or class) c

ISDB structural annotationc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/IsdbAnnotation

A spectrum structural annotation by comparison with an in-silico spectral DB, coupled to chemical and taxonomical reweighting
has super-classes
Spectrum annotation c

LCMS analysisc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LCMSAnalysis

An LCMS analysis in a given ionization mode (pos or neg)
has sub-classes
Neg LCMS analysis c, Pos LCMS analysis c

LCMS individual MS2 spectrumc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LCMSFeature

An LCMS feature from a processed LCMS analysis
has super-classes
MS2 spectrum c
is in range of
member of a specral pair op

MS2 spectrumc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/MS2Spectrum

A fragmentation mass spectrometry (or MS2) spectrum
has sub-classes
GNPS consensus MS2 spectrum c, LCMS individual MS2 spectrum c

Neg LCMS analysisc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LCMSAnalysisNeg

An LCMS analysis in negative ionization mode (pos or neg)
has super-classes
LCMS analysis c

NPCClassc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/NPCClass

A NPClassifier (NPC) chemical class
has super-classes
A chemical entity (chemical structure or class) c

NPCPathwayc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/NPCPathway

A NPClassifier (NPC) chemical pathway
has super-classes
A chemical entity (chemical structure or class) c

NPCSuperclassc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/NPCSuperclass

A NPClassifier (NPC) chemical superclass
has super-classes
A chemical entity (chemical structure or class) c

pair of GNPSConsensusSpectrac back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/CSpair

A pair of 2 GNPSConsensusSpectra
has super-classes
pair of MS2Spectra c

pair of LCMSFeaturec back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LFpair

A pair of 2 LCMSFeature
has super-classes
pair of MS2Spectra c

pair of MS2Spectrac back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/SpectralPair

A pair of 2 MS2Spectra
has sub-classes
pair of GNPSConsensusSpectra c, pair of LCMSFeature c
is in domain of
member of a specral pair op

Pos LCMS analysisc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/LCMSAnalysisPos

An LCMS analysis in positive ionization mode (pos or neg)
has super-classes
LCMS analysis c

SIRIUS structural annotationc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/SiriusStructureAnnotation

A spectrum structural annotation by SIRIUS
has super-classes
Spectrum annotation c

Spectrum annotationc back to ToC or Class ToC

IRI: https://enpkg.commons-lab.org/kg/Annotation

A spectral annotation
has sub-classes
CANOPUS chemical class annotation c, GNPS structural annotation c, ISDB structural annotation c, SIRIUS structural annotation c

Object Properties

member 1 of a spectral pairop back to ToC or Object Property ToC

IRI: https://enpkg.commons-lab.org/kg/has_member_1

The first member of a spectral pair
has super-properties
member of a specral pair op

member 2 of a spectral pairop back to ToC or Object Property ToC

IRI: https://enpkg.commons-lab.org/kg/has_member_2

The second member of a spectral pair
has super-properties
member of a specral pair op

member of a specral pairop back to ToC or Object Property ToC

IRI: https://enpkg.commons-lab.org/kg/has_member

LCMSFeature
has sub-properties
member 1 of a spectral pair op, member 2 of a spectral pair op
has domain
pair of MS2Spectra c
has range
GNPS consensus MS2 spectrum c
LCMS individual MS2 spectrum c

Named Individuals

0000 0001 9292 9463ni back to ToC or Named Individual ToC

IRI: http://orcid.org/0000-0001-9292-9463

belongs to
person c

0000 0002 3648 7362ni back to ToC or Named Individual ToC

IRI: http://orcid.org/0000-0002-3648-7362

belongs to
person c

0000 0002 9619 1707ni back to ToC or Named Individual ToC

IRI: http://orcid.org/0000-0002-9619-1707

belongs to
person c

0000 0003 3389 2191ni back to ToC or Named Individual ToC

IRI: http://orcid.org/0000-0003-3389-2191

belongs to
person c

Legend back to ToC

c: Classes
op: Object Properties
ni: Named Individuals

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.