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nmrCV-corrected-namespace.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/nmrCV#"
xml:base="http://purl.obolibrary.org/obo/nmrCV"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:doap="http://usefulinc.com/ns/doap#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:meta="http://www.co-ode.org/ontologies/meta.owl#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/nmrCV">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/nmrCV/1.2.0"/>
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
<protege:defaultLanguage xml:lang="en">en</protege:defaultLanguage>
<obo:IAO_0000112 xml:lang="en">http://nmrml.org/examples/</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level.
This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.</obo:IAO_0000115>
<obo:IAO_0000232 xml:lang="en">In case we like to be able to convert this owl CV back into the obo format, we should only use DL/owl constructs that are supported by obo. Hence, editors of this CV should take care not to use any higher descriptrion logics semantics, i.e. cardinality restrictions or defined terms using constructors. We should start to build the taxonomic backbone first and later connect the main axis via relations.
If we want to use restrictions, we should only use existential quantifiers as the OBO format does not support universal quantification.
List of terms required by current XSD (August 2013): these were bookmarked in CV (annotation property) and are visible in the new nmrTab:
CVTerm occurrences:
buffer-->buffer
solvent-->solvent
concentration standard type-->calibration compound , what is chemical shift reference ? What calibration_reference_shift under calibration compound ?
concentration standard name we here see a use-mention problem arising for the CV. The xsd should probably change here to avoid this.
encoding method (Quadrature detection method) is this the same as encoding method ?
sample container-->NMR_sample_holder
(spectrum) y axis type-->coordinate system descriptor
post acquisition solvent suppression method Two usages in xsd, but with differrent type ? -->solvent suppression method
calibration compound Two usages in xsd, but with differrent type ?-->calibration compound
data transformation method-->data transformation method
(spectral) projection method-->projection method
spectral denoising method-->spectral denoising method
window function method-->window function method
baseline correction method-->baseline correction
sample type-->NMR sample
CVParam occurrences:
file content-->data file content
software type-->software
source file type-->data file attribute (needs refactoring)
instrument configuration type-->instrument configuration
processing method type-->data processing method
CVParamType occurrences:
chemical shift standard-->chemical shift standard
solvent suppression method-->solvent suppression method
encoding scheme (Quadrature detection method)-->encoding method
window function parameter-->window function parameter
CVParamWithUnitType occurrences:
CVParamWithUnitType is currently not used in the xsd and dangling ! I assume ValueWithUnitType substitutes it ?
UserParamType occurrences:
No CV terms needed
ValueWithUnitType occurrences:
These will have to be used from the Unit ontology.</obo:IAO_0000232>
<dc:contributor xml:lang="en">Andrea Porzel</dc:contributor>
<dc:contributor xml:lang="en">Annick Moing</dc:contributor>
<dc:contributor xml:lang="en">Catherine Deborde</dc:contributor>
<dc:contributor xml:lang="en">Chris Taylor</dc:contributor>
<dc:contributor xml:lang="en">Daniel Jacob</dc:contributor>
<dc:contributor xml:lang="en">Daniel Schober</dc:contributor>
<dc:contributor xml:lang="en">David Wishart</dc:contributor>
<dc:contributor xml:lang="en">Dennis Rubtsov</dc:contributor>
<dc:contributor xml:lang="en">Helen Jenkins</dc:contributor>
<dc:contributor xml:lang="en">Irena Spasic</dc:contributor>
<dc:contributor xml:lang="en">Joseph Cruz</dc:contributor>
<dc:contributor xml:lang="en">Larissa Soldatova</dc:contributor>
<dc:contributor xml:lang="en">Michael Wilson</dc:contributor>
<dc:contributor xml:lang="en">Philippe Rocca-Serra</dc:contributor>
<dc:contributor xml:lang="en">Reza Salek</dc:contributor>
<dc:contributor xml:lang="en">Since this is a prolonged effort spanning a larger time period, there naturally were many people involved in the creation over the years and during different times.
People involved in the term creation from ID >1400000 :
This part of the NMR ontology was originally developed by the ontology working group (http://msi-ontology.sourceforge.net/) of the msi-metabolomicssociety (msi-workgroups.sf.net):
Dennis Rubtsov (Un of Cambridge, UK)
Helen Jenkins (Un of Wales, Aberystwyth, UK)
Irena Spasic (Center for Integrative Systems Biology, Manchester, UK)
Larissa Soldatova (University of Wales, Aberystwyth, UK)
Philippe Rocca-Serra (EBI and MGED Society)
Susanna-Assunta Sansone (EBI)
People involved in the term creation from ID<1400000:
Joseph Cruz
Daniel Schober
Michael Wilson
Reza Salek
Daniel Jacob
David Wishart
Terms with IDs ID<1400000 that were NOT asserted in the original Wishart obo file were created by Daniel Schober (COSMOS WP2). Its IDs were autogenerated with the Protege ID generator.
Other people that substantially helped in revising the latest and Cosmos governed CV additions were:
Michael Wilson, Wishart Group, Edmonton, Alberta, Canada
Daniel Jacob, INRA, Bordeaux, France
Annick Moing, INRA, Bordeaux, France
Catherine Deborde, INRA, Bordeaux, France
Reza Salek, EBI, Hinxton, UK
Philippe Rocca-Serra, University of Oxford, Oxford, UK
Andrea Porzel, IPB-Halle, Germany
and the COSMOS WP2 team
A paper describing the overall nmrML data standard and CV has been accepted by Analytical Chemistry (Manuscript ID: ac-2017-02795f.R1), title
`nmrML: a community supported open data standard for the description, storage, and exchange of NMR data`, author(s): Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph; Marcu, Ana; Grant, Jason; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy; Hao, Jie; Ludwig, Christian; Günther, Ulrich; Rosato, Antonio; Klein, Matthias; Lewis, Ian; Luchinat, Claudio; Jones, Andrew; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian; Viant, Mark; Wishart, David; Steinbeck, Christoph; Salek, Reza; Neumann, Steffen</dc:contributor>
<dc:contributor xml:lang="en">Steffen Neumann</dc:contributor>
<dc:contributor xml:lang="en">Susanna-Assunta Sansone</dc:contributor>
<dc:coverage xml:lang="en">Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open access nmrML XML format developed by the COSMOS EU project.</dc:coverage>
<dc:format xml:lang="en">OWL</dc:format>
<dc:license xml:lang="en">https://creativecommons.org/licenses/by/4.0/</dc:license>
<dc:title xml:lang="en">nuclear magnetic resonance CV</dc:title>
<doap:audience xml:lang="en">This CV is to be used by metabolomics researchers, or basically any chenomics or proteomics researchers who apply the nmrML xml to store their NMRraw data in a vendor agnostic manner. But nmrML can also be used to capture experimental results and (limited) basic metadata like molecule to spectral feature assignments.</doap:audience>
<doap:bug-database xml:lang="en">https://github.com/nmrML/nmrML/issues</doap:bug-database>
<doap:documenter xml:lang="en">Daniel Schober</doap:documenter>
<doap:implements xml:lang="en">https://github.com/nmrML/nmrML</doap:implements>
<doap:location xml:lang="en">https://github.com/nmrML/nmrML/tree/master/ontologies</doap:location>
<doap:mailing-list xml:lang="en">https://groups.google.com/forum/?hl=en#!forum/nmrml/join</doap:mailing-list>
<doap:maintainer xml:lang="en">http://www.metabolomics-msi.org/
http://phenomenal-h2020.eu/home/
http://www.cosmos-fp7.eu/WP2</doap:maintainer>
<oboInOwl:auto-generated-by xml:lang="en">OBO-Edit 2.2</oboInOwl:auto-generated-by>
<oboInOwl:created_by xml:lang="en">Daniel Schober</oboInOwl:created_by>
<oboInOwl:creation_date xml:lang="en">2017-10-19T10:11:26Z</oboInOwl:creation_date>
<rdfs:comment xml:lang="en">This version (1.1.0) uses the Basic Formal Ontology (BFO) as its top level ontology. We might at some point close the resulting semantic gap by using OBI and IAO as intermediate bridges.</rdfs:comment>
<owl:deprecated xml:lang="en">http://www.metabolomicscentre.ca/nmrML/msi-nmr.obo</owl:deprecated>
<owl:versionInfo xml:lang="en">1.1.0</owl:versionInfo>
<foaf:homepage xml:lang="en">http://nmrml.org/cv/</foaf:homepage>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
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<owl:AnnotationProperty rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
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<rdfs:label xml:lang="en">definition</rdfs:label>
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<rdfs:label xml:lang="en">database_cross_reference</rdfs:label>
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<!-- http://www.w3.org/2000/01/rdf-schema#comment -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
<!-- http://www.w3.org/2000/01/rdf-schema#label -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
<!-- http://www.w3.org/2004/02/skos/core#altLabel -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#altLabel"/>
<!-- http://www.w3.org/2004/02/skos/core#definition -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#definition"/>
<!-- http://www.w3.org/2004/02/skos/core#editorialNote -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#editorialNote"/>
<!-- http://www.w3.org/2004/02/skos/core#example -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#example"/>
<!-- http://www.w3.org/2004/02/skos/core#scopeNote -->
<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#scopeNote"/>
<!-- http://xmlns.com/foaf/0.1/homepage -->
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
<rdfs:label>entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
<rdfs:label>process</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
<rdfs:label>realizable entity</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:label>quality</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/BFO_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
<rdfs:label>generically dependent continuant</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000336"/>
<obo:IAO_0000115>For 1r/1i spectra and for Bruker, this term describe an array of integers (32bits).</obo:IAO_0000115>
<rdfs:label xml:lang="en">integer32</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000548"/>
<obo:IAO_0000115 xml:lang="en">A reference number relevant to the sample under study.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">MSI:NMR</obo:IAO_0000116>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:string</oboInOwl:hasDbXref>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000001</oboInOwl:id>
<rdfs:label xml:lang="en">sample number</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000001"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:string</owl:annotatedTarget>
<rdfs:label xml:lang="en">The allowed value-type for this CV term.</rdfs:label>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000336"/>
<obo:IAO_0000115>For 1r/1i spectra and for Bruker, this term describe an array of longs (64bits).</obo:IAO_0000115>
<rdfs:label xml:lang="en">long64</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000548"/>
<obo:IAO_0000115 xml:lang="en">The chemical phase of a pure sample, or the state of a mixed sample.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">MSI:NMR</obo:IAO_0000116>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000003</oboInOwl:id>
<rdfs:label xml:lang="en">sample state information</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000004">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000548"/>
<obo:IAO_0000115 xml:lang="en">Total mass of sample used.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">MSI:NMR</obo:IAO_0000116>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:float</oboInOwl:hasDbXref>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000004</oboInOwl:id>
<rdfs:label xml:lang="en">sample mass information</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000004"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:float</owl:annotatedTarget>
<rdfs:label xml:lang="en">The allowed value-type for this CV term.</rdfs:label>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000005">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000548"/>
<obo:IAO_0000115 xml:lang="en">Total volume of solution used.</obo:IAO_0000115>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:float</oboInOwl:hasDbXref>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000005</oboInOwl:id>
<rdfs:label xml:lang="en">sample volume</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000005"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:float</owl:annotatedTarget>
<rdfs:label xml:lang="en">The allowed value-type for this CV term.</rdfs:label>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000006 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000006">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000548"/>
<obo:IAO_0000115 xml:lang="en">Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">MSI:NMR</obo:IAO_0000116>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:float</oboInOwl:hasDbXref>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000006</oboInOwl:id>
<rdfs:label xml:lang="en">sample concentration</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000006"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:float</owl:annotatedTarget>
<rdfs:label xml:lang="en">The allowed value-type for this CV term.</rdfs:label>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000008 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000008">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400042"/>
<obo:IAO_0000115>One of the problems that should be apparent after observing the spectrum and the FID is that it is not possible
to determine if the frequency is positive or negative. The instrument uses a spectrometer
frequency and all signal frequencies are measured relative to the spectrometer frequency. If a molecule
produces two signals, one at 300,000,001 Hz and another at 299,999,999 Hz, and the spectrometer frequency
is 300,000,000 Hz, the first signal is at +1 Hz and the second is at -1 Hz. Electronically the lower frequency
signals are very easy frequency to detect, transmit, amplify and sample.
The complication with this rotating frame of reference is that a single detector can not distinguish positive and
negative frequencies. This problem is why quadrature detection is important. Quadrature detection uses two detector channels
separated by 90 degrees. These are referred to as the real channel and the imaginary channel. Using these
two channels, it is possible to distinguish positive and negative frequencies. This section shows how the
quadrature signal is processed to obtain an NMR spectrum.
The Fourier transform produces a complex number with a real and an imaginary component. The Re function
extracts the real spectrum and the Im function extracts the imaginary spectrum from the complex number.</obo:IAO_0000115>
<rdfs:label xml:lang="en">quadrature detection</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000010">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000585"/>
<rdfs:label xml:lang="en">contact role</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000011">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:label xml:lang="en">data file attribute</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000012 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000012">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000496"/>
<rdfs:label xml:lang="en">NMR instrument type</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000172"/>
<rdfs:label xml:lang="en">1D spectrum coordinate system descriptor</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000014">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400063"/>
<rdfs:label xml:lang="en">pre-acquisition solvent suppression</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400038"/>
<rdfs:label xml:lang="en">peak processing</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000016">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000167"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000330"/>
<rdfs:label xml:lang="en">Hexafluorobenzene</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000017">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000330"/>
<obo:IAO_0000118>CDCl3</obo:IAO_0000118>
<rdfs:label xml:lang="en">Chloroform-d</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000018 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000018">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000330"/>
<obo:IAO_0000118>D2O</obo:IAO_0000118>
<oboInOwl:consider>CHEBI:41981</oboInOwl:consider>
<rdfs:label xml:lang="en">heavy water</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000019">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1002011"/>
<rdfs:label xml:lang="en">sample pH</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000020">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1002011"/>
<rdfs:label xml:lang="en">post buffer pH</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000021 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000021">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400041"/>
<obo:IAO_0000115>Apodization is an umbrella term that is used to refer to signal processing covering the manipulation of the FID to either increase signal-to-noise (S/N) or resolution. it is usually possible to gain either S/N or resolution, but not both.
Apodization is usually performed by applying a window function to the FID</obo:IAO_0000115>
<obo:IAO_0000117>Philippe Rocca-Serra</obo:IAO_0000117>
<obo:IAO_0000119>http://www.scs.illinois.edu/nmr/handouts/general_pdf/ugi034.pdf</obo:IAO_0000119>
<rdfs:label>apodization</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000878"/>
<obo:IAO_0000119>http://www.metabolomicssociety.org/databases</obo:IAO_0000119>
<rdfs:label xml:lang="en">metabolomics database identifier</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000023">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000022"/>
<rdfs:label xml:lang="en">Metabolights identifier</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000024 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000024">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000026"/>
<rdfs:label xml:lang="en">acetonitrile</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000025 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000025">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000026"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000030"/>
<rdfs:label xml:lang="en">1,4-Dioxane</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000026">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400033"/>
<rdfs:label xml:lang="en">1H spectrum reference compound</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000026"/>
<obo:IAO_0000118>DSS</obo:IAO_0000118>
<rdfs:label xml:lang="en">2,2-Dimethyl-2-silapentane-5-sulfonate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000028 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000028">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000026"/>
<rdfs:label xml:lang="en">sodium acetate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000029">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000026"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000030"/>
<obo:IAO_0000118>TMS</obo:IAO_0000118>
<rdfs:label xml:lang="en">tetramethylsilane</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000030">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400033"/>
<rdfs:label xml:lang="en">13C spectrum reference compound</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000031">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000496"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Instrument model name not including the vendor's name.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">MSI:NMR</obo:IAO_0000116>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000031</oboInOwl:id>
<rdfs:label xml:lang="en">NMR instrument model</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000032">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000496"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Free text description of a single customization made to the instrument; for several modifications, use several entries.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">MSI:NMR</obo:IAO_0000116>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:string</oboInOwl:hasDbXref>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000032</oboInOwl:id>
<rdfs:label xml:lang="en">instrument customization</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000032"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:string</owl:annotatedTarget>
<rdfs:label xml:lang="en">The allowed value-type for this CV term.</rdfs:label>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000033">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000030"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000431"/>
<rdfs:label xml:lang="en">Chloroform-d1</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400117"/>
<rdfs:label>keyword</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000035 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000035">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000030"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000036"/>
<rdfs:label xml:lang="en">tetramethylammonium bromide</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000036">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400033"/>
<rdfs:label xml:lang="en">15N spectrum reference compound</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000037 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000037">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000036"/>
<rdfs:label xml:lang="en">ammonia (liquid)</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000038 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000038">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000036"/>
<rdfs:label xml:lang="en">ammonium bromide</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000039 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000039">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000036"/>
<rdfs:label xml:lang="en">1,4-morpholine</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000040 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000040">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000036"/>
<rdfs:label xml:lang="en">nitromethane</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000041 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000041">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000036"/>
<rdfs:label xml:lang="en">pyridine</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000042 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000042">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000036"/>
<rdfs:label xml:lang="en">sodium nitrate</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000043 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000043">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1400073"/>
<obo:IAO_0000118>solvent filtering</obo:IAO_0000118>
<rdfs:label xml:lang="en">post-acquisition solvent suppression</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000044 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000044">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1001954"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Nuclear magnetic resonance decoupling (NMR decoupling for short) is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate fully or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks which are up to several hertz frequency from each other. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds.</obo:IAO_0000115>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_decoupling</obo:IAO_0000119>
<rdfs:label xml:lang="en">decoupling method</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000045 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000045">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000044"/>
<rdfs:label xml:lang="en">homonuclear decoupling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000046 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000046">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000044"/>
<rdfs:label xml:lang="en">heteronuclear decoupling</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000047 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000047">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000049"/>
<obo:IAO_0000115 xml:lang="en">State if the sample is in emulsion form.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000047</oboInOwl:id>
<rdfs:label xml:lang="en">emulsion</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000048 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000048">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000003"/>
<obo:IAO_0000115 xml:lang="en">State if the sample is in gaseous form.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000048</oboInOwl:id>
<rdfs:label xml:lang="en">gas</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000049 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000049">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000003"/>
<obo:IAO_0000115 xml:lang="en">State if the sample is in liquid form.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000049</oboInOwl:id>
<rdfs:label xml:lang="en">liquid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000050 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000050">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000003"/>
<obo:IAO_0000115 xml:lang="en">State if the sample is in solid form.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000050</oboInOwl:id>
<rdfs:label xml:lang="en">solid</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000051 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000051">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000049"/>
<obo:IAO_0000115 xml:lang="en">State if the sample is in solution form.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000051</oboInOwl:id>
<rdfs:label xml:lang="en">solution</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000052 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000052">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000049"/>
<obo:IAO_0000115 xml:lang="en">State if the sample is in suspension form.</obo:IAO_0000115>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000052</oboInOwl:id>
<rdfs:label xml:lang="en">suspension</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/nmrCV_1000053 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/nmrCV_1000053">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000548"/>
<obo:IAO_0000115 xml:lang="en">Sample batch lot identifier.</obo:IAO_0000115>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:string</oboInOwl:hasDbXref>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMR:1000053</oboInOwl:id>
<rdfs:label xml:lang="en">sample batch information</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/nmrCV_1000053"/>
<owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">value-type:xsd:string</owl:annotatedTarget>
<rdfs:label xml:lang="en">The allowed value-type for this CV term.</rdfs:label>
</owl:Axiom>