From 3614f795e5f7187070fdbba2ce4250fae02eb522 Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Wed, 21 Jun 2023 16:33:07 +0200 Subject: [PATCH 01/12] add absorbance to class template --- src/templates/vibso_classes.tsv | 53 +++++++++++++++++---------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 0aa8f00..ac9f345 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -1,34 +1,35 @@ id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment 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 SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| 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 integration time setting integration time|integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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 accumulations number of acquisitions https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. owl:Class setting datum ORCID:0000-0002-1595-3213 This class might 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 groove frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range owl:Class physical quality ORCID:0000-0002-1595-3213 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) -obo:VIBSO_0000010 groove density setting grating|grating 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_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 integration time setting integration time|integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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 accumulations number of acquisitions https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. owl:Class setting datum ORCID:0000-0002-1595-3213 This class might 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 groove frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range owl:Class physical quality ORCID:0000-0002-1595-3213 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) +obo:VIBSO_0000010 groove density setting grating|grating 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_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 magnification|magnification 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. + 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. obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. owl:Class scalar measurement datum ORCID:0000-0001-7694-5519 200 mW The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot. -obo:VIBSO_0000018 region of interest imaging region of interest|ROI https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 owl:Class site ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 -obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the width (length in the X direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 1 mm region of interest width = (point distance X) * (number of measurements X) -obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the height (length in the Y direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.5 mm region of interest breadth = (point distance Y) * (number of measurements Y) -obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the depth (length in the Z direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.1 mm region of interest depth = (point distance Z) * (number of measurements Z) -obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 20 µm point distance X = (region of interest width) / (number of measurements X) -obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Y = (region of interest breadth) / (number of measurements Y) -obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Z = (region of interest depth) / (number of measurements Z) -obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) -obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) +obo:VIBSO_0000018 region of interest imaging region of interest|ROI https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 owl:Class site ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 +obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the width (length in the X direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 1 mm region of interest width = (point distance X) * (number of measurements X) +obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the height (length in the Y direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.5 mm region of interest breadth = (point distance Y) * (number of measurements Y) +obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the depth (length in the Z direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.1 mm region of interest depth = (point distance Z) * (number of measurements Z) +obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 20 µm point distance X = (region of interest width) / (number of measurements X) +obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Y = (region of interest breadth) / (number of measurements Y) +obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Z = (region of interest depth) / (number of measurements Z) +obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) +obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. -Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) \ No newline at end of file +Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) +obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class meassurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. From b45c4d71819ae04fa980352bd87c594edbcbcdb5 Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Wed, 21 Jun 2023 16:38:12 +0200 Subject: [PATCH 02/12] fix typo --- src/templates/vibso_classes.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index ac9f345..0beff9d 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -20,7 +20,7 @@ example:objective_magnification_factor_setting_for_RamanSpectrometerX rdf:type o 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. -obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. owl:Class scalar measurement datum ORCID:0000-0001-7694-5519 200 mW The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot. +obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. owl:Class scalar measurement datum ORCID:0000-0001-7694-5519 200 mW The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot. obo:VIBSO_0000018 region of interest imaging region of interest|ROI https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 owl:Class site ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the width (length in the X direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 1 mm region of interest width = (point distance X) * (number of measurements X) obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the height (length in the Y direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.5 mm region of interest breadth = (point distance Y) * (number of measurements Y) @@ -32,4 +32,4 @@ obo:VIBSO_0000025 number of measurements X number of points in the X direction|n obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class meassurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. From 646d82912aab6c01d580f0c5a194f7c5bb34d19f Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Wed, 21 Jun 2023 16:53:59 +0200 Subject: [PATCH 03/12] add mapping annotation to TSV template and AFO --- src/ontology/components/vibso_classes.owl | 15 +++++++++++++++ src/templates/vibso_classes.tsv | 10 +++++----- 2 files changed, 20 insertions(+), 5 deletions(-) diff --git a/src/ontology/components/vibso_classes.owl b/src/ontology/components/vibso_classes.owl index 6e24443..d9b0d09 100644 --- a/src/ontology/components/vibso_classes.owl +++ b/src/ontology/components/vibso_classes.owl @@ -31,6 +31,7 @@ Declaration(Class(obo:BFO_0000029)) Declaration(Class(obo:CHMO_0000823)) Declaration(Class(obo:IAO_0000027)) Declaration(Class(obo:IAO_0000032)) +Declaration(Class(obo:IAO_0000109)) Declaration(Class(obo:IAO_0000140)) Declaration(Class(obo:OBI_0000654)) Declaration(Class(obo:OBI_0000968)) @@ -63,6 +64,7 @@ Declaration(Class(obo:VIBSO_0000024)) Declaration(Class(obo:VIBSO_0000025)) Declaration(Class(obo:VIBSO_0000026)) Declaration(Class(obo:VIBSO_0000027)) +Declaration(Class(obo:VIBSO_0000028)) Declaration(ObjectProperty(obo:BFO_0000050)) Declaration(AnnotationProperty(obo:IAO_0000112)) Declaration(AnnotationProperty(obo:IAO_0000115)) @@ -72,6 +74,7 @@ Declaration(AnnotationProperty(obo:IAO_0000231)) Declaration(AnnotationProperty(obo:IAO_0100001)) Declaration(AnnotationProperty(dc:contributor)) Declaration(AnnotationProperty(dc:source)) +Declaration(AnnotationProperty(skos:exactMatch)) @@ -401,5 +404,17 @@ AnnotationAssertion(rdfs:label obo:VIBSO_0000027 "number of measurements Z"@en) AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000027 ) SubClassOf(obo:VIBSO_0000027 obo:IAO_0000140) +# Class: obo:VIBSO_0000028 (absorbance meassurement datum) + +AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) obo:IAO_0000115 obo:VIBSO_0000028 "A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power."@en) +AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "absorbance"@en) +AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "extinction"@en) +AnnotationAssertion(dc:contributor obo:VIBSO_0000028 ) +AnnotationAssertion(rdfs:comment obo:VIBSO_0000028 "Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping."@en) +AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "absorbance meassurement datum"@en) +AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000028 ) +AnnotationAssertion(skos:exactMatch obo:VIBSO_0000028 ) +SubClassOf(obo:VIBSO_0000028 obo:IAO_0000109) + ) \ No newline at end of file diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 0beff9d..63f9c91 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -1,8 +1,8 @@ -id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment 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 SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001 +id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment editor note obsoleted obsolescence reason term replaced by exact mapping broad mapping narrow mapping +ID AL rdfs:label@en AL IAO:0000118@en SPLIT=| AI rdfs:seeAlso SPLIT=| AL IAO:0000115@en >AI dc11:source SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001 AI skos:exactMatch SPLIT=| AI skos:broadMatch SPLIT=| AI skos:narrowMatch SPLIT=| 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 integration time setting integration time|integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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_0000002 integration time setting integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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. @@ -10,7 +10,7 @@ obo:VIBSO_0000006 device temperature setting https://github.com/NFDI4Chem/Vibra obo:VIBSO_0000007 number of accumulations number of acquisitions https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. owl:Class setting datum ORCID:0000-0002-1595-3213 This class might 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 groove frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range owl:Class physical quality ORCID:0000-0002-1595-3213 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) -obo:VIBSO_0000010 groove density setting grating|grating 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_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. @@ -32,4 +32,4 @@ obo:VIBSO_0000025 number of measurements X number of points in the X direction|n obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 The definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. http://purl.allotrope.org/ontologies/result#AFR_0001157 From 59466ae36aa2c748d726d616d3296766ec6797e9 Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Thu, 22 Jun 2023 11:52:02 +0200 Subject: [PATCH 04/12] Revert "add mapping annotation to TSV template and AFO" This reverts commit bb940b9d11080f86d6ae822f27583c3460169f47. --- src/ontology/components/vibso_classes.owl | 15 --------------- src/templates/vibso_classes.tsv | 6 +++--- 2 files changed, 3 insertions(+), 18 deletions(-) diff --git a/src/ontology/components/vibso_classes.owl b/src/ontology/components/vibso_classes.owl index d9b0d09..6e24443 100644 --- a/src/ontology/components/vibso_classes.owl +++ b/src/ontology/components/vibso_classes.owl @@ -31,7 +31,6 @@ Declaration(Class(obo:BFO_0000029)) Declaration(Class(obo:CHMO_0000823)) Declaration(Class(obo:IAO_0000027)) Declaration(Class(obo:IAO_0000032)) -Declaration(Class(obo:IAO_0000109)) Declaration(Class(obo:IAO_0000140)) Declaration(Class(obo:OBI_0000654)) Declaration(Class(obo:OBI_0000968)) @@ -64,7 +63,6 @@ Declaration(Class(obo:VIBSO_0000024)) Declaration(Class(obo:VIBSO_0000025)) Declaration(Class(obo:VIBSO_0000026)) Declaration(Class(obo:VIBSO_0000027)) -Declaration(Class(obo:VIBSO_0000028)) Declaration(ObjectProperty(obo:BFO_0000050)) Declaration(AnnotationProperty(obo:IAO_0000112)) Declaration(AnnotationProperty(obo:IAO_0000115)) @@ -74,7 +72,6 @@ Declaration(AnnotationProperty(obo:IAO_0000231)) Declaration(AnnotationProperty(obo:IAO_0100001)) Declaration(AnnotationProperty(dc:contributor)) Declaration(AnnotationProperty(dc:source)) -Declaration(AnnotationProperty(skos:exactMatch)) @@ -404,17 +401,5 @@ AnnotationAssertion(rdfs:label obo:VIBSO_0000027 "number of measurements Z"@en) AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000027 ) SubClassOf(obo:VIBSO_0000027 obo:IAO_0000140) -# Class: obo:VIBSO_0000028 (absorbance meassurement datum) - -AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) obo:IAO_0000115 obo:VIBSO_0000028 "A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power."@en) -AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "absorbance"@en) -AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "extinction"@en) -AnnotationAssertion(dc:contributor obo:VIBSO_0000028 ) -AnnotationAssertion(rdfs:comment obo:VIBSO_0000028 "Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping."@en) -AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "absorbance meassurement datum"@en) -AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000028 ) -AnnotationAssertion(skos:exactMatch obo:VIBSO_0000028 ) -SubClassOf(obo:VIBSO_0000028 obo:IAO_0000109) - ) \ No newline at end of file diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 63f9c91..bdf9515 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -1,5 +1,5 @@ -id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment editor note obsoleted obsolescence reason term replaced by exact mapping broad mapping narrow mapping -ID AL rdfs:label@en AL IAO:0000118@en SPLIT=| AI rdfs:seeAlso SPLIT=| AL IAO:0000115@en >AI dc11:source SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001 AI skos:exactMatch SPLIT=| AI skos:broadMatch SPLIT=| AI skos:narrowMatch SPLIT=| +id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment 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 SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| 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 integration time setting integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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. @@ -32,4 +32,4 @@ obo:VIBSO_0000025 number of measurements X number of points in the X direction|n obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 The definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. http://purl.allotrope.org/ontologies/result#AFR_0001157 +obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. From e9422cc01c939c9a66601fa5aeaadd7f553b4967 Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Thu, 22 Jun 2023 11:58:10 +0200 Subject: [PATCH 05/12] fix typo --- src/templates/vibso_classes.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index bdf9515..bbd26a2 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -31,5 +31,5 @@ obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling ste obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. -Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 absorbance meassurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) +obo:VIBSO_0000028 absorbance measurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. From 33ec9de546aca87a85577f2e8ede76aaf9507ede Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Thu, 22 Jun 2023 13:50:33 +0200 Subject: [PATCH 06/12] recreate vibso owl components --- src/ontology/components/vibso_classes.owl | 19 ++++++++++++++++--- .../components/vibso_object_properties.owl | 9 +++------ 2 files changed, 19 insertions(+), 9 deletions(-) diff --git a/src/ontology/components/vibso_classes.owl b/src/ontology/components/vibso_classes.owl index 6e24443..5c4dac5 100644 --- a/src/ontology/components/vibso_classes.owl +++ b/src/ontology/components/vibso_classes.owl @@ -24,13 +24,14 @@ Prefix(Wikipedia:=) Ontology( - -Annotation(rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_classes.tsv' template.") + +Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_classes.tsv', which is edited manually by domain experts.") Declaration(Class(obo:BFO_0000029)) Declaration(Class(obo:CHMO_0000823)) Declaration(Class(obo:IAO_0000027)) Declaration(Class(obo:IAO_0000032)) +Declaration(Class(obo:IAO_0000109)) Declaration(Class(obo:IAO_0000140)) Declaration(Class(obo:OBI_0000654)) Declaration(Class(obo:OBI_0000968)) @@ -63,6 +64,7 @@ Declaration(Class(obo:VIBSO_0000024)) Declaration(Class(obo:VIBSO_0000025)) Declaration(Class(obo:VIBSO_0000026)) Declaration(Class(obo:VIBSO_0000027)) +Declaration(Class(obo:VIBSO_0000028)) Declaration(ObjectProperty(obo:BFO_0000050)) Declaration(AnnotationProperty(obo:IAO_0000112)) Declaration(AnnotationProperty(obo:IAO_0000115)) @@ -401,5 +403,16 @@ AnnotationAssertion(rdfs:label obo:VIBSO_0000027 "number of measurements Z"@en) AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000027 ) SubClassOf(obo:VIBSO_0000027 obo:IAO_0000140) +# Class: obo:VIBSO_0000028 (absorbance measurement datum) -) \ No newline at end of file +AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) obo:IAO_0000115 obo:VIBSO_0000028 "A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power."@en) +AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "absorbance"@en) +AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "extinction"@en) +AnnotationAssertion(dc:contributor obo:VIBSO_0000028 ) +AnnotationAssertion(rdfs:comment obo:VIBSO_0000028 "Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping."@en) +AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "absorbance measurement datum"@en) +AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000028 ) +SubClassOf(obo:VIBSO_0000028 obo:IAO_0000109) + + +) diff --git a/src/ontology/components/vibso_object_properties.owl b/src/ontology/components/vibso_object_properties.owl index b8a0617..ce57cf3 100644 --- a/src/ontology/components/vibso_object_properties.owl +++ b/src/ontology/components/vibso_object_properties.owl @@ -24,9 +24,6 @@ Prefix(Wikipedia:=) Ontology( - -Annotation(rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_object_properties.tsv' template.") - - - -) \ No newline at end of file + +Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_object_properties.tsv', which is edited manually by domain experts.") +) From ac8f85f56c27c1fddea4561a104a1d594754f5a4 Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Thu, 22 Jun 2023 14:03:18 +0200 Subject: [PATCH 07/12] change label to just absorbance, as the definition makes clear this is not a quality but a measurement --- src/ontology/components/vibso_classes.owl | 5 ++--- src/templates/vibso_classes.tsv | 4 ++-- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/src/ontology/components/vibso_classes.owl b/src/ontology/components/vibso_classes.owl index 5c4dac5..82528a3 100644 --- a/src/ontology/components/vibso_classes.owl +++ b/src/ontology/components/vibso_classes.owl @@ -403,14 +403,13 @@ AnnotationAssertion(rdfs:label obo:VIBSO_0000027 "number of measurements Z"@en) AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000027 ) SubClassOf(obo:VIBSO_0000027 obo:IAO_0000140) -# Class: obo:VIBSO_0000028 (absorbance measurement datum) +# Class: obo:VIBSO_0000028 (absorbance) AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) obo:IAO_0000115 obo:VIBSO_0000028 "A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power."@en) -AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "absorbance"@en) AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "extinction"@en) AnnotationAssertion(dc:contributor obo:VIBSO_0000028 ) AnnotationAssertion(rdfs:comment obo:VIBSO_0000028 "Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping."@en) -AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "absorbance measurement datum"@en) +AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "absorbance"@en) AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000028 ) SubClassOf(obo:VIBSO_0000028 obo:IAO_0000109) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index bbd26a2..217ca99 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -31,5 +31,5 @@ obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling ste obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. -Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 absorbance measurement datum extinction|absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) +obo:VIBSO_0000028 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. From f2d32bd394378a824c67fff0b7fa556fe5bb106d Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Fri, 23 Jun 2023 09:39:21 +0200 Subject: [PATCH 08/12] update definition --- src/ontology/components/vibso_classes.owl | 8 +++----- src/templates/vibso_classes.tsv | 5 +++++ 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/src/ontology/components/vibso_classes.owl b/src/ontology/components/vibso_classes.owl index 82528a3..5c5d0a4 100644 --- a/src/ontology/components/vibso_classes.owl +++ b/src/ontology/components/vibso_classes.owl @@ -24,14 +24,13 @@ Prefix(Wikipedia:=) Ontology( - + Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_classes.tsv', which is edited manually by domain experts.") Declaration(Class(obo:BFO_0000029)) Declaration(Class(obo:CHMO_0000823)) Declaration(Class(obo:IAO_0000027)) Declaration(Class(obo:IAO_0000032)) -Declaration(Class(obo:IAO_0000109)) Declaration(Class(obo:IAO_0000140)) Declaration(Class(obo:OBI_0000654)) Declaration(Class(obo:OBI_0000968)) @@ -405,13 +404,12 @@ SubClassOf(obo:VIBSO_0000027 obo:IAO_0000140) # Class: obo:VIBSO_0000028 (absorbance) -AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) obo:IAO_0000115 obo:VIBSO_0000028 "A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power."@en) -AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "extinction"@en) +AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) obo:IAO_0000115 obo:VIBSO_0000028 "A data item that quantifies the absorption quality of a sample by being the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption)."@en) AnnotationAssertion(dc:contributor obo:VIBSO_0000028 ) AnnotationAssertion(rdfs:comment obo:VIBSO_0000028 "Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping."@en) AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "absorbance"@en) AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000028 ) -SubClassOf(obo:VIBSO_0000028 obo:IAO_0000109) +SubClassOf(obo:VIBSO_0000028 obo:IAO_0000027) ) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 217ca99..932a692 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -31,5 +31,10 @@ obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling ste obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 "A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. +<<<<<<< HEAD Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) obo:VIBSO_0000028 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +======= +Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) +obo:VIBSO_0000028 absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption quality of a sample by being the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class data item| ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +>>>>>>> 7d24ea3 (update definition) From 97d64a6a4117ebbb3986e3a529549001ab611b18 Mon Sep 17 00:00:00 2001 From: StroemPhi Date: Fri, 23 Jun 2023 10:26:57 +0200 Subject: [PATCH 09/12] refine definition and add subclass of axiom relating this to its PATO quality --- src/ontology/components/vibso_classes.owl | 5 ++++- src/templates/vibso_classes.tsv | 4 ++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/src/ontology/components/vibso_classes.owl b/src/ontology/components/vibso_classes.owl index 5c5d0a4..9ad54a6 100644 --- a/src/ontology/components/vibso_classes.owl +++ b/src/ontology/components/vibso_classes.owl @@ -35,6 +35,7 @@ Declaration(Class(obo:IAO_0000140)) Declaration(Class(obo:OBI_0000654)) Declaration(Class(obo:OBI_0000968)) Declaration(Class(obo:PATO_0001018)) +Declaration(Class(obo:PATO_0001293)) Declaration(Class(obo:VIBSO_0000000)) Declaration(Class(obo:VIBSO_0000001)) Declaration(Class(obo:VIBSO_0000002)) @@ -65,6 +66,7 @@ Declaration(Class(obo:VIBSO_0000026)) Declaration(Class(obo:VIBSO_0000027)) Declaration(Class(obo:VIBSO_0000028)) Declaration(ObjectProperty(obo:BFO_0000050)) +Declaration(ObjectProperty(obo:IAO_0000136)) Declaration(AnnotationProperty(obo:IAO_0000112)) Declaration(AnnotationProperty(obo:IAO_0000115)) Declaration(AnnotationProperty(obo:IAO_0000116)) @@ -404,12 +406,13 @@ SubClassOf(obo:VIBSO_0000027 obo:IAO_0000140) # Class: obo:VIBSO_0000028 (absorbance) -AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) obo:IAO_0000115 obo:VIBSO_0000028 "A data item that quantifies the absorption quality of a sample by being the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption)."@en) +AnnotationAssertion(Annotation(dc:source ) Annotation(dc:source ) Annotation(dc:source Wikipedia:Absorbance) obo:IAO_0000115 obo:VIBSO_0000028 "A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption)."@en) AnnotationAssertion(dc:contributor obo:VIBSO_0000028 ) AnnotationAssertion(rdfs:comment obo:VIBSO_0000028 "Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping."@en) AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "absorbance"@en) AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000028 ) SubClassOf(obo:VIBSO_0000028 obo:IAO_0000027) +SubClassOf(obo:VIBSO_0000028 ObjectSomeValuesFrom(obo:IAO_0000136 obo:PATO_0001293)) ) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 932a692..532a207 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -36,5 +36,9 @@ Together with the focal point distance, this setting defines the region of inter obo:VIBSO_0000028 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A meassurement datum that represents the logarithm to the base 10 (linear absorbance) of the incident (prior to absorption) spectral radiant power, divided by the transmitted spectral radiant power. https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class measurement datum ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. ======= Together with the focal point distance, this setting defines the region of interest depth." owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) +<<<<<<< HEAD obo:VIBSO_0000028 absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption quality of a sample by being the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157 owl:Class data item| ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. >>>>>>> 7d24ea3 (update definition) +======= +obo:VIBSO_0000028 absorbance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157|https://en.wikipedia.org/wiki/Absorbance owl:Class data item|('is about' some obo:PATO_0001293) ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +>>>>>>> 5b14450 (refine definition and add subclass of axiom relating this to its PATO quality) From 5b7fb101dbf592ae12f1235412b4b20117aac7a9 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Fri, 9 Aug 2024 09:48:58 +0200 Subject: [PATCH 10/12] beautify table --- src/templates/vibso_classes.tsv | 62 ++++++++++++++++----------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index b942fc3..2780216 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -1,34 +1,34 @@ id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment 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 SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| 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 integration time setting integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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 accumulations number of acquisitions https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. owl:Class setting datum ORCID:0000-0002-1595-3213 This class might 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 groove frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range owl:Class physical quality ORCID:0000-0002-1595-3213 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) -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_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 integration time setting integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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 accumulations number of acquisitions https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. owl:Class setting datum ORCID:0000-0002-1595-3213 This class might 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 groove frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range owl:Class physical quality ORCID:0000-0002-1595-3213 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) +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 magnification|magnification 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 100x -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. -obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. owl:Class scalar measurement datum ORCID:0000-0001-7694-5519 200 mW The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot. -obo:VIBSO_0000018 region of interest imaging region of interest|ROI https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 owl:Class site ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 -obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the width (length in the X direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 1 mm region of interest width = (point distance X) * (number of measurements X) -obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the height (length in the Y direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.5 mm region of interest breadth = (point distance Y) * (number of measurements Y) -obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the depth (length in the Z direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.1 mm region of interest depth = (point distance Z) * (number of measurements Z) -obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 20 µm point distance X = (region of interest width) / (number of measurements X) -obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Y = (region of interest breadth) / (number of measurements Y) -obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Z = (region of interest depth) / (number of measurements Z) -obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) -obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements Y = (region of interest breadth) / (point distance Y) -obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157|https://en.wikipedia.org/wiki/Absorbance owl:Class data item|('is about' some obo:PATO_0001293) ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. -obo:VIBSO_0000028 Raman raw data raw Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam. https://wiki.charisma.ideaconsult.net/wiki/Item:Q64 owl:Class measurement datum ORCID:0000-0002-2239-3955 -obo:VIBSO_0000029 lens numerical aperture numerical aperture https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76 A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located. https://wiki.charisma.ideaconsult.net/wiki/Item:Q385|https://en.wikipedia.org/wiki/Numerical_aperture owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm. possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA -obo:VIBSO_000030 primary Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 A data item that is obtained by processing raw Raman data. owl:Class 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 +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 magnification|magnification 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 100x +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. +obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. owl:Class scalar measurement datum ORCID:0000-0001-7694-5519 200 mW The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot. +obo:VIBSO_0000018 region of interest imaging region of interest|ROI https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 owl:Class site ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 +obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the width (length in the X direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 1 mm region of interest width = (point distance X) * (number of measurements X) +obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the height (length in the Y direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.5 mm region of interest breadth = (point distance Y) * (number of measurements Y) +obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the depth (length in the Z direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.1 mm region of interest depth = (point distance Z) * (number of measurements Z) +obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 20 µm point distance X = (region of interest width) / (number of measurements X) +obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Y = (region of interest breadth) / (number of measurements Y) +obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Z = (region of interest depth) / (number of measurements Z) +obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) +obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements Y = (region of interest breadth) / (point distance Y) +obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) +obo:VIBSO_0000028 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157|https://en.wikipedia.org/wiki/Absorbance owl:Class data item|('is about' some obo:PATO_0001293) ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +obo:VIBSO_0000028 Raman raw data raw Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam. https://wiki.charisma.ideaconsult.net/wiki/Item:Q64 owl:Class measurement datum ORCID:0000-0002-2239-3955 +obo:VIBSO_0000029 lens numerical aperture numerical aperture https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76 A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located. https://wiki.charisma.ideaconsult.net/wiki/Item:Q385|https://en.wikipedia.org/wiki/Numerical_aperture owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm. possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA +obo:VIBSO_000030 primary Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 A data item that is obtained by processing raw Raman data. owl:Class 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 From 2f0519945b36b1ad38de4393af65195742d74d62 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:50:45 +0200 Subject: [PATCH 11/12] change IRI --- src/templates/vibso_classes.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 69aca03..8b0f66d 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -28,7 +28,7 @@ obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling ste obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements Y = (region of interest breadth) / (point distance Y) obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157|https://en.wikipedia.org/wiki/Absorbance owl:Class data item|('is about' some obo:PATO_0001293) ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. obo:VIBSO_0000028 Raman raw data raw Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam. https://wiki.charisma.ideaconsult.net/wiki/Item:Q64 owl:Class measurement datum ORCID:0000-0002-2239-3955 obo:VIBSO_0000029 lens numerical aperture numerical aperture https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76 A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located. https://wiki.charisma.ideaconsult.net/wiki/Item:Q385|https://en.wikipedia.org/wiki/Numerical_aperture owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm. possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA obo:VIBSO_0000030 primary Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 A data item that is obtained by processing raw Raman data. owl:Class 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 +obo:VIBSO_0000031 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157|https://en.wikipedia.org/wiki/Absorbance owl:Class data item|('is about' some obo:PATO_0001293) ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. From d7945b42c588ebc160cf69e58347be3835d2be0d Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Mon, 11 Nov 2024 07:51:59 +0100 Subject: [PATCH 12/12] sort columns --- src/templates/vibso_classes.tsv | 68 ++++++++++++++++----------------- 1 file changed, 34 insertions(+), 34 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 8b0f66d..f72bc2f 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -1,34 +1,34 @@ -id label alternative term link(s) to issue(s) definition definition source URI type super class contributor URI example of usage comment 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 SPLIT=| TYPE SC % SPLIT=| AI dc11:contributor SPLIT=| AL IAO:0000112@en AL rdfs:comment@en SPLIT=| 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 integration time setting integration period setting https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i 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 accumulations number of acquisitions https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. owl:Class setting datum ORCID:0000-0002-1595-3213 This class might 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 groove frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range owl:Class physical quality ORCID:0000-0002-1595-3213 temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) -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 magnification|magnification 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 100x -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. -obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. owl:Class scalar measurement datum ORCID:0000-0001-7694-5519 200 mW The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot. -obo:VIBSO_0000018 region of interest imaging region of interest|ROI https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 owl:Class site ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 -obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the width (length in the X direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 1 mm region of interest width = (point distance X) * (number of measurements X) -obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the height (length in the Y direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.5 mm region of interest breadth = (point distance Y) * (number of measurements Y) -obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the depth (length in the Z direction) of the region of interest. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 0.1 mm region of interest depth = (point distance Z) * (number of measurements Z) -obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 20 µm point distance X = (region of interest width) / (number of measurements X) -obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Y = (region of interest breadth) / (number of measurements Y) -obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 10 µm point distance Z = (region of interest depth) / (number of measurements Z) -obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 50 number of measurements X = (region of interest width) / (point distance X) -obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 100 number of measurements Y = (region of interest breadth) / (point distance Y) -obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth. owl:Class setting datum ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 10 number of measurements Z = (region of interest depth) / (point distance Z) -obo:VIBSO_0000028 Raman raw data raw Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam. https://wiki.charisma.ideaconsult.net/wiki/Item:Q64 owl:Class measurement datum ORCID:0000-0002-2239-3955 -obo:VIBSO_0000029 lens numerical aperture numerical aperture https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76 A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located. https://wiki.charisma.ideaconsult.net/wiki/Item:Q385|https://en.wikipedia.org/wiki/Numerical_aperture owl:Class setting datum ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm. possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA -obo:VIBSO_0000030 primary Raman data https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 A data item that is obtained by processing raw Raman data. owl:Class 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 -obo:VIBSO_0000031 absorbance extinction https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157|https://en.wikipedia.org/wiki/Absorbance owl:Class data item|('is about' some obo:PATO_0001293) ORCID:0000-0002-1595-3213 Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. +id label alternative term super class definition definition source URI comment example of usage editor note obsoleted obsolescence reason term replaced by contributor URI link(s) to issue(s) type +ID AL rdfs:label@en AL IAO:0000118@en SPLIT=| SC % SPLIT=| AL IAO:0000115@en >AI dc11:source SPLIT=| AL rdfs:comment@en SPLIT=| AL IAO:0000112@en AL IAO:0000116@en SPLIT=| AT owl:deprecated^^xsd:boolean AI IAO:0000231 AI IAO:0100001 AI dc11:contributor SPLIT=| AI rdfs:seeAlso SPLIT=| TYPE +obo:VIBSO_0000000 vibrational spectrometer configuration specification setting datum A setting datum that specifies the needed settings of a spectrometer used in vibrational spectroscopy. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/39 owl:Class +obo:VIBSO_0000001 Raman spectrometer configuration device setting 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, ...). The set of meassured configuration characteristics of a Raman spectrometer, like the operating temperature of a Raman spectrometer. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/47 owl:Class +obo:VIBSO_0000002 integration time setting integration period setting setting datum A setting datum that specifies the length of time that a photo detector is allowed to collect photons before passing the accumulated charge to the A/D converter for processing. The minimum integration time is the shortest integration time the device supports and is dependent on how fast the detector can read out all of the pixel information. Integration time should not be confused with data transfer speed. https://www.oceaninsight.com/knowledge-hub/glossary/#i This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/40 owl:Class +obo:VIBSO_0000003 preamplifier gain setting setting datum A setting datum that specifies the preamplifier gain in CCD sensors. This class should better be defined in a more general device ontology. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/41 owl:Class +obo:VIBSO_0000004 horizontal shift speed setting setting datum A setting datum that specifies the horizontal shift speed in CCD sensors. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 owl:Class +obo:VIBSO_0000005 vertical shift speed setting setting datum A setting datum that specifies the vertical shift speed in CCD sensors. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42 owl:Class +obo:VIBSO_0000006 device temperature setting setting datum A setting datum that specifies the operating temperature of a device. This class should better be defined in a more general device ontology. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/43 owl:Class +obo:VIBSO_0000007 number of accumulations number of acquisitions setting datum A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio. This class might better be defined in a more general device ontology. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30 owl:Class +obo:VIBSO_0000008 CCD sensor binning read mode setting setting datum A setting datum that specifies the binning read mode of a device with a CCD sensor. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/46 owl:Class +obo:VIBSO_0000009 groove density groove frequency physical quality A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter. Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541) ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 owl:Class +obo:VIBSO_0000010 groove density setting setting datum A setting datum that specifies the number of grooves in a diffraction grating device. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45 owl:Class +obo:VIBSO_0000011 diffraction grating device 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 This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/49 owl:Class +obo:VIBSO_0000012 deprecated_excitation wavelength A physical quality of the light source that is used used to excite a system to a higher energy state. 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 ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 owl:Class +obo:VIBSO_0000013 excitation wavelength setting setting datum 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. This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/48 owl:Class +obo:VIBSO_0000014 objective magnification factor setting magnification|magnification setting setting datum A setting datum that specifies the magnification factor of the objective collecting the scattered light. 100x ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/24 owl:Class +obo:VIBSO_0000015 spectral window range maximum acquisition band maximum data item|('part of' some 'Raman spectrum') 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. 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. ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 owl:Class +obo:VIBSO_0000016 spectral window range minimum acquisition band minimum data item|('part of' some 'Raman spectrum') 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. 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. ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/31 owl:Class +obo:VIBSO_0000017 incident light power datum excitation light power|light power on the sample scalar measurement datum A scalar measurement datum that is the result of measuring the incoming light power before the sample holder and which depends on the laser power and on the dispersive behaviour of the filters and optical components. The incident power is an elementary measurement parameter allowing to compare among measurements conducted with the same setup. A thorough investigation of the effects of light irradiation onto the sample depends on the local irradiance (power per unit area) and requires deeper knowledge of the irradiation geometry, e.g. width, depth and shape of the focal spot. 200 mW ORCID:0000-0001-7694-5519 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/29 owl:Class +obo:VIBSO_0000018 region of interest imaging region of interest|ROI site A site that refers to a user-defined portion of the image area in which data will be acquired. The remainder of the image area will be discarded. https://wiki.charisma.ideaconsult.net/wiki/Item:Q57 See also https://w3id.org/reproduceme#ROI & http://purl.obolibrary.org/obo/NCIT_C85402 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000019 region of interest width ROI width|ROI horizontal length setting datum A setting datum that specifies the width (length in the X direction) of the region of interest. region of interest width = (point distance X) * (number of measurements X) 1 mm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000020 region of interest breadth ROI breadth|ROI lateral length setting datum A setting datum that specifies the height (length in the Y direction) of the region of interest. region of interest breadth = (point distance Y) * (number of measurements Y) 0.5 mm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000021 region of interest depth ROI depth|ROI vertical length setting datum A setting datum that specifies the depth (length in the Z direction) of the region of interest. region of interest depth = (point distance Z) * (number of measurements Z) 0.1 mm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000022 point distance X sampling pace in the X direction|sampling step in the X direction|voxel distance in the X direction setting datum A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the X direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. point distance X = (region of interest width) / (number of measurements X) 20 µm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000023 point distance Y sampling pace in the Y direction|sampling step in the Y direction|voxel distance in the Y direction setting datum A setting datum that specifies the equal distance which the incident light beam will be moved laterally in the Y direction on a given sample within the region of interest after each measurement, when performing a spatially resolved spectroscopy. point distance Y = (region of interest breadth) / (number of measurements Y) 10 µm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000024 point distance Z sampling pace in the Z direction|sampling step in the Z direction|voxel distance in the Z direction|vertical mapping distance|axial mapping distance setting datum A setting datum that specifies the equal distance which the incident light beam will moved along the focal axis within the region of interest, when performing a spatially resolved spectroscopy. point distance Z = (region of interest depth) / (number of measurements Z) 10 µm ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000025 number of measurements X number of points in the X direction|number of points per line setting datum A setting datum that specifies how many equally configured measurements of a sample are to be performed along the X-axis of a certain region of interest. Together with the point distance X, this setting defines the region of interest width. number of measurements X = (region of interest width) / (point distance X) 50 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000026 number of measurements Y number of points in the Y direction|number of lines per layer setting datum A setting datum that specifies how many equally configured measurements of a sample are to be performed along the Y-axis of a certain region of interest. Together with the point distance Y, this setting defines the region of interest breadth. number of measurements Y = (region of interest breadth) / (point distance Y) 100 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000027 number of measurements Z number of points in the Z direction|number of layers per acquisition setting datum A setting datum that specifies how many equally configured measurements of a sample are to be performed in the vertical direction (on the Z-axis) of a certain region of interest. Together with the focal point distance, this setting defines the region of interest depth. number of measurements Z = (region of interest depth) / (point distance Z) 10 ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3956 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32 owl:Class +obo:VIBSO_0000028 Raman raw data raw Raman data measurement datum A measurement datum that is obtained from a calibrated and ready Raman spectrometer and prior to be submitted to any mathematical modification. The only corrections on the data shall be the one associated with the spectrometer. The data will assign pixels readouts with nm as per calibration of the spectrometer and a.u. as intensity readout but will not be corrected in relationship of the incident monochromatic beam. https://wiki.charisma.ideaconsult.net/wiki/Item:Q64 ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77 owl:Class +obo:VIBSO_0000029 lens numerical aperture numerical aperture setting datum A setting datum that, as a dimensionless number, represents the quality which characterizes the range of angles over which an optical system can accept or emit light [dc:source wikidata:Numerical_aperture]. It gets calculated by the sine of one half of the vertex angle of the largest cone of meridional rays that can enter or leave an optical system or element, multiplied by the refractive index of the medium in which the cone is located. https://wiki.charisma.ideaconsult.net/wiki/Item:Q385|https://en.wikipedia.org/wiki/Numerical_aperture The light was focused onto the embedded sample using a 100× objective with a numerical aperture of 0.9, resulting in a diffraction-limited in-plane laser spot size of <1 μm. possible equivalents in other terminologies: http://purl.obolibrary.org/obo/NCIT_C181921 & https://w3id.org/reproduceme#LensNA ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/76 owl:Class +obo:VIBSO_0000030 primary Raman data 'data item'|(is_specified_output_of some ('data transformation' and (has_specified_input some 'Raman raw data'))) A data item that is obtained by processing raw Raman data. ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/132 owl:Class +obo:VIBSO_0000031 absorbance extinction data item|('is about' some obo:PATO_0001293) A data item that quantifies the absorption of light by some material as the logarithm of the incident electromagnetic radiation power (before absorption), divided by the transmitted electromagnetic radiation power (after absorption). https://doi.org/10.1351/goldbook|http://purl.allotrope.org/ontologies/result#AFR_0001157|https://en.wikipedia.org/wiki/Absorbance Definition was adapted from “afo:absorbance“. We did not reuse/import this AFO term directly due to the associated ontological commitment of AFO. Yet, we will provide a mapping. ORCID:0000-0002-1595-3213 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86 owl:Class