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Add VIBSO:0000015 & VIBSO:0000016 (spectral window range minimum/maximum) & "alternative label" TSV column #55

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Feb 2, 2023
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Add VIBSO:0000015 & VIBSO:0000016 (spectral window range minimum/maximum) & "alternative label" TSV column #55

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bd3fb7e
Add new terms according to #31 & add column to TSV
StroemPhi Feb 2, 2023
8cb48ef
Recreate the OWL components
StroemPhi Feb 2, 2023
b7b836b
Allow multiple alternative terms in the TSV template
StroemPhi Feb 2, 2023
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33 changes: 32 additions & 1 deletion src/ontology/components/vibso_classes.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,11 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)


Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_classes.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2023-01-09/components/vibso_classes.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2023-02-02/components/vibso_classes.owl>
Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_classes.tsv', which is edited manually by domain experts."^^xsd:string)

Declaration(Class(obo:CHMO_0000823))
Declaration(Class(obo:IAO_0000027))
Declaration(Class(obo:IAO_0000140))
Declaration(Class(obo:OBI_0000654))
Declaration(Class(obo:OBI_0000968))
Expand All @@ -45,10 +47,13 @@ Declaration(Class(obo:VIBSO_0000011))
Declaration(Class(obo:VIBSO_0000012))
Declaration(Class(obo:VIBSO_0000013))
Declaration(Class(obo:VIBSO_0000014))
Declaration(Class(obo:VIBSO_0000015))
Declaration(Class(obo:VIBSO_0000016))
Declaration(ObjectProperty(obo:BFO_0000050))
Declaration(AnnotationProperty(obo:IAO_0000112))
Declaration(AnnotationProperty(obo:IAO_0000115))
Declaration(AnnotationProperty(obo:IAO_0000116))
Declaration(AnnotationProperty(obo:IAO_0000118))
Declaration(AnnotationProperty(obo:IAO_0000231))
Declaration(AnnotationProperty(obo:IAO_0100001))
Declaration(AnnotationProperty(dc:contributor))
Expand Down Expand Up @@ -203,5 +208,31 @@ AnnotationAssertion(rdfs:label obo:VIBSO_0000014 "objective magnification factor
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000014 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24%20>)
SubClassOf(obo:VIBSO_0000014 obo:IAO_0000140)

# Class: obo:VIBSO_0000015 (spectral window range maximum)

AnnotationAssertion(obo:IAO_0000112 obo:VIBSO_0000015 "210 cm^-1"@en)
AnnotationAssertion(obo:IAO_0000115 obo:VIBSO_0000015 "A data item that is the part of a Raman spectrum which represents the maximum wavenumber included in the spectrum and which is calculated from the windows size and window center."@en)
AnnotationAssertion(obo:IAO_0000116 obo:VIBSO_0000015 "It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived."@en)
AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000015 "acquisition band maximum"@en)
AnnotationAssertion(dc:contributor obo:VIBSO_0000015 <http://orcid.org/0000-0001-7694-5519>)
AnnotationAssertion(dc:contributor obo:VIBSO_0000015 <http://orcid.org/0000-0002-1595-3213>)
AnnotationAssertion(rdfs:label obo:VIBSO_0000015 "spectral window range maximum"@en)
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000015 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31>)
SubClassOf(obo:VIBSO_0000015 obo:IAO_0000027)
SubClassOf(obo:VIBSO_0000015 ObjectSomeValuesFrom(obo:BFO_0000050 obo:CHMO_0000823))

# Class: obo:VIBSO_0000016 (spectral window range minimum)

AnnotationAssertion(obo:IAO_0000112 obo:VIBSO_0000016 "1960 cm^-1"@en)
AnnotationAssertion(obo:IAO_0000115 obo:VIBSO_0000016 "A data item that is the part of a Raman spectrum which represents the minimum wavenumber included in the spectrum and which is calculated from the windows size and window center."@en)
AnnotationAssertion(obo:IAO_0000116 obo:VIBSO_0000016 "It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived."@en)
AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000016 "acquisition band minimum"@en)
AnnotationAssertion(dc:contributor obo:VIBSO_0000016 <http://orcid.org/0000-0001-7694-5519>)
AnnotationAssertion(dc:contributor obo:VIBSO_0000016 <http://orcid.org/0000-0002-1595-3213>)
AnnotationAssertion(rdfs:label obo:VIBSO_0000016 "spectral window range minimum"@en)
AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000016 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31>)
SubClassOf(obo:VIBSO_0000016 obo:IAO_0000027)
SubClassOf(obo:VIBSO_0000016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:CHMO_0000823))


)
2 changes: 1 addition & 1 deletion src/ontology/components/vibso_object_properties.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)


Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_object_properties.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2023-01-09/components/vibso_object_properties.owl>
<http://purl.obolibrary.org/obo/vibso/releases/2023-02-02/components/vibso_object_properties.owl>
Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_object_properties.tsv', which is edited manually by domain experts."^^xsd:string)


Expand Down
36 changes: 19 additions & 17 deletions src/templates/vibso_classes.tsv
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Original file line number Diff line number Diff line change
@@ -1,20 +1,22 @@
id label link(s) to issue(s) definition definition source URI type super class contributor URI example of usage editor note obsoleted obsolescence reason term replaced by
ID AL rdfs:label@en AI rdfs:seeAlso SPLIT=| AL IAO:0000115@en >AI dc11:source TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001
obo:VIBSO_0000000 vibrational spectrometer configuration specification https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/39 A setting datum that specifies the needed settings of a spectrometer used in vibrational spectroscopy. owl:Class setting datum ORCID:0000-0002-1595-3213
obo:VIBSO_0000001 Raman spectrometer configuration https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/47 A device setting that represents the measured or set physical qualities which make up the configuration state of a Raman spectrometer at the time of a measurement (e.g. operating temperature, exitation wavelength, groove density, ...). owl:Class device setting ORCID:0000-0002-1595-3213 The set of meassured configuration characteristics of a Raman spectrometer, like the operating temperature of a Raman spectrometer.
obo:VIBSO_0000002 exposure time setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the duration in which an electromagnetic radiation beam is exposed to / recorded by a photosensor. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000003 preamplifier gain setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/41 A setting datum that specifies the preamplifier gain in CCD sensors. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology.
obo:VIBSO_0000004 horizontal shift speed setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 A setting datum that specifies the horizontal shift speed in CCD sensors. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000005 vertical shift speed setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 A setting datum that specifies the vertical shift speed in CCD sensors. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000006 device temperature setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/43 A setting datum that specifies the operating temperature of a device. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology.
obo:VIBSO_0000007 number of scans setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/44 A setting datum that specifies the number of iterations performed in a spectroscopic meassurement from which an aggregated assay output is generated. owl:Class setting datum|('part of' some 'vibrational spectrometer configuration specification') ORCID:0000-0002-1595-3213 The setting entered into a Raman microscope which specifies the desired number of measurements this Raman microscope has to perform to produce an usable Raman spectrum. This class should better be defined in a more general device ontology.
obo:VIBSO_0000008 CCD sensor binning read mode setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/46 A setting datum that specifies the binning read mode of a device with a CCD sensor. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000009 groove density https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality of a diffraction grating that represents the number of grooves per length unit (e.g. mm) on the surface that causes the diffraction of the light. Wikipedia:Diffraction_grating owl:Class physical quality ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000010 groove density setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A setting datum that specifies the number of grooves in a diffraction grating device. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000011 diffraction grating https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/49 A device that is an optical component with a periodic structure that diffracts light into several beams travelling in different directions (i.e. different diffraction angles) https://en.wikipedia.org/wiki/Diffraction_grating owl:Class device ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000012 deprecated_excitation wavelength https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 A physical quality of the light source that is used used to excite a system to a higher energy state. owl:Class ORCID:0000-0002-1595-3213 This class is not needed, as PATO:wavelength is sufficient, if this quality of a Raman device is really needed. true failed exploratory term wavelength
obo:VIBSO_0000013 excitation wavelength setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 A setting datum that specifies the wavelength of an electromagnetic radiation source (e.g. a laser) which has the function to excite the energy state of a target material. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000014 objective magnification factor setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24 A setting datum that specifies the magnification factor of the objective collecting the scattered light. owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 "example:RamanSpectrometerX rdf:type obo:CHMO_0001235 (Raman spectrometer) ;
id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage editor note obsoleted obsolescence reason term replaced by
ID AL rdfs:label@en AL IAO:0000118@en SPLIT=| AI rdfs:seeAlso SPLIT=| AL IAO:0000115@en >AI dc11:source TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001
obo:VIBSO_0000000 vibrational spectrometer configuration specification https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/39 A setting datum that specifies the needed settings of a spectrometer used in vibrational spectroscopy. owl:Class setting datum ORCID:0000-0002-1595-3213
obo:VIBSO_0000001 Raman spectrometer configuration https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/47 A device setting that represents the measured or set physical qualities which make up the configuration state of a Raman spectrometer at the time of a measurement (e.g. operating temperature, exitation wavelength, groove density, ...). owl:Class device setting ORCID:0000-0002-1595-3213 The set of meassured configuration characteristics of a Raman spectrometer, like the operating temperature of a Raman spectrometer.
obo:VIBSO_0000002 exposure time setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the duration in which an electromagnetic radiation beam is exposed to / recorded by a photosensor. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000003 preamplifier gain setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/41 A setting datum that specifies the preamplifier gain in CCD sensors. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology.
obo:VIBSO_0000004 horizontal shift speed setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 A setting datum that specifies the horizontal shift speed in CCD sensors. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000005 vertical shift speed setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 A setting datum that specifies the vertical shift speed in CCD sensors. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000006 device temperature setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/43 A setting datum that specifies the operating temperature of a device. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology.
obo:VIBSO_0000007 number of scans setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/44 A setting datum that specifies the number of iterations performed in a spectroscopic meassurement from which an aggregated assay output is generated. owl:Class setting datum|('part of' some 'vibrational spectrometer configuration specification') ORCID:0000-0002-1595-3213 The setting entered into a Raman microscope which specifies the desired number of measurements this Raman microscope has to perform to produce an usable Raman spectrum. This class should better be defined in a more general device ontology.
obo:VIBSO_0000008 CCD sensor binning read mode setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/46 A setting datum that specifies the binning read mode of a device with a CCD sensor. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000009 groove density https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality of a diffraction grating that represents the number of grooves per length unit (e.g. mm) on the surface that causes the diffraction of the light. Wikipedia:Diffraction_grating owl:Class physical quality ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000010 groove density setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A setting datum that specifies the number of grooves in a diffraction grating device. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000011 diffraction grating https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/49 A device that is an optical component with a periodic structure that diffracts light into several beams travelling in different directions (i.e. different diffraction angles) https://en.wikipedia.org/wiki/Diffraction_grating owl:Class device ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000012 deprecated_excitation wavelength https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 A physical quality of the light source that is used used to excite a system to a higher energy state. owl:Class ORCID:0000-0002-1595-3213 This class is not needed, as PATO:wavelength is sufficient, if this quality of a Raman device is really needed. true failed exploratory term wavelength
obo:VIBSO_0000013 excitation wavelength setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 A setting datum that specifies the wavelength of an electromagnetic radiation source (e.g. a laser) which has the function to excite the energy state of a target material. owl:Class setting datum ORCID:0000-0002-1595-3213 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.
obo:VIBSO_0000014 objective magnification factor setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24 A setting datum that specifies the magnification factor of the objective collecting the scattered light. owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 "example:RamanSpectrometerX rdf:type obo:CHMO_0001235 (Raman spectrometer) ;
obo:OBI_0000293 (has_specified_input) example:objective_magnification_factor_setting_for_RamanSpectrometerX .
example:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type obo:VIBSO_0000014 ;
obo:OBI_0002815 (has representation) '100 x' ."
obo:VIBSO_0000015 spectral window range maximum acquisition band maximum https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 A data item that is the part of a Raman spectrum which represents the maximum wavenumber included in the spectrum and which is calculated from the windows size and window center. owl:Class data item|('part of' some 'Raman spectrum') ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 210 cm^-1 It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived.
obo:VIBSO_0000016 spectral window range minimum acquisition band minimum https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 A data item that is the part of a Raman spectrum which represents the minimum wavenumber included in the spectrum and which is calculated from the windows size and window center. owl:Class data item|('part of' some 'Raman spectrum') ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 1960 cm^-1 It needs to be determined, if this is also part of another kind of spectrum, such as a vibrational spectrum in general. We also need to decide, if we need to also model the terms window size and window center, from which this term is derived.