@prefix : <http://purl.allotrope.org/voc/afo/domain/REC/2026/03/chromatography-ms#> .
@prefix cl: <http://purl.obolibrary.org/obo/CL> .
@prefix go: <http://purl.obolibrary.org/obo/GO> .
@prefix ro: <http://purl.obolibrary.org/obo/RO> .
@prefix bfo: <http://purl.obolibrary.org/obo/BFO> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix iao: <http://purl.obolibrary.org/obo/IAO> .
@prefix obi: <http://purl.obolibrary.org/obo/OBI> .
@prefix ops: <http://www.openphacts.org/units/> .
@prefix ore: <http://www.openarchives.org/ore/terms/> .
@prefix org: <http://www.w3.org/ns/org#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix pav: <http://purl.org/pav/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xml: <http://www.w3.org/xml/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix af-c: <http://purl.allotrope.org/ontologies/common#> .
@prefix af-e: <http://purl.allotrope.org/ontologies/equipment#> .
@prefix af-m: <http://purl.allotrope.org/ontologies/material#> .
@prefix af-p: <http://purl.allotrope.org/ontologies/process#> .
@prefix af-q: <http://purl.allotrope.org/ontologies/quality#> .
@prefix af-r: <http://purl.allotrope.org/ontologies/result#> .
@prefix af-x: <http://purl.allotrope.org/ontologies/property#> .
@prefix chmo: <http://purl.obolibrary.org/obo/CHMO> .
@prefix envo: <http://purl.obolibrary.org/obo/ENVO> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix ncit: <http://purl.obolibrary.org/obo/NCIT> .
@prefix pato: <http://purl.obolibrary.org/obo/PATO> .
@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 time: <http://www.w3.org/2006/time#> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix af-cq: <http://purl.allotrope.org/ontologies/common/qualifier#> .
@prefix af-fn: <http://purl.allotrope.org/ontologies/function#> .
@prefix af-re: <http://purl.allotrope.org/ontologies/realizable#> .
@prefix af-rl: <http://purl.allotrope.org/ontologies/role#> .
@prefix chebi: <http://purl.obolibrary.org/obo/CHEBI> .
@prefix af-cur: <http://purl.allotrope.org/ontologies/curation#> .
@prefix af-math: <http://purl.allotrope.org/ontologies/math#> .
@prefix af-ec-001: <http://purl.allotrope.org/ontologies/equipment/codelist/001#> .
@prefix af-ec-002: <http://purl.allotrope.org/ontologies/equipment/codelist/002#> .
@prefix af-ec-003: <http://purl.allotrope.org/ontologies/equipment/codelist/003#> .
@prefix af-ec-004: <http://purl.allotrope.org/ontologies/equipment/codelist/004#> .
@prefix af-ec-005: <http://purl.allotrope.org/ontologies/equipment/codelist/005#> .
@prefix af-ec-006: <http://purl.allotrope.org/ontologies/equipment/codelist/006#> .
@base <http://purl.allotrope.org/voc/afo/domain/REC/2026/03/chromatography-ms#> .

<http://purl.allotrope.org/voc/afo/domain/REC/2026/03/chromatography-ms> rdf:type owl:Ontology ;
                                                                                    owl:versionIRI <http://purl.allotrope.org/voc/afo/domain/REC/2026/03/chromatography-ms> ;
                                                                                    owl:imports <http://purl.allotrope.org/voc/afo/REC/2026/03/afo> ,
                                                                                                <http://purl.allotrope.org/voc/afo/domain/REC/2026/03/chromatography> ,
                                                                                                <http://purl.allotrope.org/voc/afo/domain/REC/2026/03/mass-spectrometry> ;
                                                                                    dct:contributor <http://www.allotrope.org> ;
                                                                                    dct:issued "2026-03-30T12:00:00Z"^^xsd:dateTime ;
                                                                                    dct:license <http://purl.allotrope.org/voc/creative-commons-attribution-license> ;
                                                                                    dct:modified "2025-12-16T12:00:00Z"^^xsd:dateTime ;
                                                                                    dct:publisher <http://www.allotrope.org> ;
                                                                                    dct:rights <http://purl.allotrope.org/voc/attribution> ,
                                                                                               <http://purl.allotrope.org/voc/copyright> ;
                                                                                    dct:rightsHolder <http://www.allotrope.org> ;
                                                                                    dct:title "AFO Chromatography-MS Domain Ontology (REC/2026/03)" ;
                                                                                    owl:priorVersion <http://purl.allotrope.org/voc/afo/domain/REC/2025/12/chromatography-ms> ;
                                                                                    owl:versionInfo "REC/2026/03" .

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

###  http://purl.allotrope.org/ontologies/result#AFR_0000035
af-r:AFR_0000035 rdf:type owl:Class ;
                 rdfs:subClassOf af-r:AFR_0000160 ,
                                 af-r:AFR_0002543 ;
                 af-x:AFX_0002808 <http://purl.obolibrary.org/obo/MS_1001472> ;
                 dct:source <https://en.wikipedia.org/wiki/Mass_chromatogram> ;
                 skos:altLabel "SIM chromatogram" ,
                               "SIM spectrum" ;
                 skos:definition "A selected-ion monitoring (SIM) chromatogram is similar to an XIC, with the exception that the mass spectrometer is operated in SIM mode, such that only preselected m/z values are detected in the analysis. [Wikipedia]" ;
                 skos:prefLabel "selected ion monitoring chromatogram" .


###  http://purl.allotrope.org/ontologies/result#AFR_0000079
af-r:AFR_0000079 rdf:type owl:Class ;
                 rdfs:subClassOf af-r:AFR_0000160 ;
                 skos:altLabel "SIC chromatogram" ;
                 skos:definition "A plot of ion current vs. retention time obtained from a chromatography experiment with mass detection. A small mass window is monitored such that the mass chromatogram represents detection of a very specific mass-to-charge ratio. [CHMO]" ;
                 skos:prefLabel "selected ion current chromatogram" .


###  http://purl.allotrope.org/ontologies/result#AFR_0000204
af-r:AFR_0000204 rdf:type owl:Class ;
                 rdfs:subClassOf af-r:AFR_0000443 ;
                 dct:source <https://en.wikipedia.org/wiki/Mass_chromatogram> ;
                 skos:altLabel "EIC" ,
                               "XIC" ;
                 skos:definition "In an extracted-ion chromatogram (XIC or EIC), also called a reconstructed-ion chromatogram (RIC), one or more m/z values representing one or more analytes of interest are recovered ('extracted') from the entire data set for a chromatographic run. [Wikipedia]" ;
                 skos:prefLabel "extracted ion chromatogram" .


###  http://purl.allotrope.org/ontologies/result#AFR_0000443
af-r:AFR_0000443 rdf:type owl:Class ;
                 rdfs:subClassOf af-r:AFR_0000160 ,
                                 af-r:AFR_0002542 ;
                 skos:definition "A ion chromatogram is a distribution function of a ion current signal of a mass detector versus time of acquisition or versus volume of analyte. [Allotrope]" ;
                 skos:prefLabel "ion chromatogram" .


###  http://purl.allotrope.org/ontologies/result#AFR_0001950
af-r:AFR_0001950 rdf:type owl:Class ;
                 rdfs:subClassOf af-r:AFR_0001060 ;
                 skos:altLabel "3-dimensional mass spectra" ,
                               "3-dimensional mass spectrum" ,
                               "3D mass spectra" ,
                               "3D mass spectrum" ,
                               "three dimensional mass spectra" ,
                               "three dimensional mass spectrum" ,
                               "three-dimensional mass spectra" ;
                 skos:definition "A three-dimensional mass spectrum is a data distribution function of counts versus m/z and versus time obtained by counting the ions produced by a sample as a function of their mass-to-charge ratio and as a function of time. [Allotrope]" ;
                 skos:prefLabel "three-dimensional mass spectrum" .


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

###  http://www.allotrope.org
<http://www.allotrope.org> rdf:type owl:NamedIndividual ,
                                    foaf:Organization ;
                           foaf:name "Allotrope Foundation" .


###  http://purl.allotrope.org/voc/attribution
<http://purl.allotrope.org/voc/attribution> rdf:type owl:NamedIndividual ,
                                                     dct:RightsStatement ;
                                            dct:description """
These taxonomies contain material or may constitute derivative works of material which may be subject to copyright by one of the following organizations.  By using these taxonomies, you agree to the following terms and conditions applicable to its contents:
******************************************************************************
Copyright Notice and Terms for IUPAC Gold Book
______________________________________________________________________________
Copyright © 1998, Regents of the University of California
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
******************************************************************************
Copyright Notice and Terms for PSI-MS (Proteomics Standards Initiative - Mass Spectrometry) Mass spectrometer output files and spectra interpretation
_____________________________________________________________________________
Created by Matt Chambers, Andreas Bertsch, Marius Kallhardt, Eric Deutsch Fredrik Levander, Pierre-Alain Binz, and Gerhard Mayer. Publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group. This work is used pursuant to a Creative Commons license available here: http://creativecommons.org/licenses/by/3.0/legalcode

******************************************************************************
Attribution Notice for National Center for Biomedical Ontology materials.

This work contains material from the Cell Ontology and Clinical Measurement Ontology, available here: http://bioportal.bioontology.org/.
******************************************************************************
Attribution Notice for ChEBI
This work contains material from the European Bioinformatics Institute’s ChEBI database.
******************************************************************************
Attribution Notice for Quantities Units Dimensions Data Types (http://www.qudt.org/)
This work contains content from www.qudt.org and is used pursuant to a Creative Commons License available here: http://creativecommons.org/licenses/by-sa/3.0/us/legalcode. The original work may have been modified.
******************************************************************************
Copyright and Attribution Notice for Dublin Core Metadata Initiative Document
This work contains material from the following DCMI document used pursuant to a creative commons license available here: https://creativecommons.org/licenses/by/4.0/legalcode. This material may have been modified or changed.
Timestamped URL:          http://dublincore.org/documents/2012/06/14/dcmi-terms/
Date Issued:                       2012-06-14
Document Status:            This is a DCMI Recommendation.
Copyright © 1995-2015 DCMI. All Rights Reserved. DCMI liability, trademark/service mark, document use and software licensing rules apply.
******************************************************************************

""" ;
                                            dct:title "Derivative works attribution" .


###  http://purl.allotrope.org/voc/copyright
<http://purl.allotrope.org/voc/copyright> rdf:type owl:NamedIndividual ,
                                                   dct:RightsStatement ;
                                          dct:description "Copyright © 2015-2026 Allotrope Foundation" ;
                                          dct:rightsHolder <http://www.allotrope.org> ;
                                          dct:title "Copyright © 2015-2026 Allotrope Foundation" .


###  http://purl.allotrope.org/voc/creative-commons-attribution-license
<http://purl.allotrope.org/voc/creative-commons-attribution-license> rdf:type owl:NamedIndividual ,
                                                                              dct:LicenseDocument ;
                                                                     dct:description """This work is licensed under a Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/.

THESE MATERIALS ARE PROVIDED \"AS IS\" AND ALLOTROPE EXPRESSLY DISCLAIMS ALL WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, TITLE, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

Copyright © 2015-2026 Allotrope Foundation
""" ;
                                                                     dct:title "Creative Commons Attribution 4.0 International Public License" .


###  http://purl.allotrope.org/voc/afo/domain/CR/2018/04/lc-uv
<http://purl.allotrope.org/voc/afo/domain/CR/2018/04/lc-uv> rdf:type owl:NamedIndividual ;
                                                            dct:rightsHolder <http://www.allotrope.org> .


###  Generated by the OWL API (version 5.5.1) https://github.com/owlcs/owlapi/