From 5209a26e9927c9a3114182c9c58ca1341c4aaed4 Mon Sep 17 00:00:00 2001 From: Giacomo Lanza <37865804+Zack-83@users.noreply.github.com> Date: Fri, 8 Nov 2024 18:31:40 +0100 Subject: [PATCH] Sort logically columns (#145) * sort columns (most useful left, constant ones right) * reshape also properties table * prettify examples table --- src/templates/vibso_classes.tsv | 98 +++++++++++------------ src/templates/vibso_examples.tsv | 16 ++-- src/templates/vibso_object_properties.tsv | 4 +- 3 files changed, 59 insertions(+), 59 deletions(-) diff --git a/src/templates/vibso_classes.tsv b/src/templates/vibso_classes.tsv index 22d93f1..d06a0f6 100644 --- a/src/templates/vibso_classes.tsv +++ b/src/templates/vibso_classes.tsv @@ -1,49 +1,49 @@ -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_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 setting datum that specifies the upper boundary of the spectral window range utilized during the acquisition of spectroscopic data. owl:Class setting datum 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 setting datum that specifies the lower boundary of the spectral window range utilized during the acquisition of spectroscopic data. owl:Class setting datum 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_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 resolution https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A physical quality of a measurement device that expresses (realizes) the device's capacity to distinguish between two distinct but closely related measurements of the same physical quality or type, often quantified as the smallest detectable difference (resolution interval) between measured values. owl:Class physical quality ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000032 resolution interval https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A data item that quantifies a resolution, by representing the minimum measurable difference between two measurements of the same physical quality or type, such that the measurements can be distinguished as different. owl:Class data item|'is about' some resolution|'has value specification' some 'value specification' ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000033 resolution power https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A ratio that quantifies the ability of a measurement device to distinguish between small differences in measurement values, expressed as the ratio between a typical measurement datum and the corresponding resolution interval. ISBN 081946043-5 owl:Class ratio ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000034 spatial resolution interval https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A resolution interval that quantifies the minimum distance between two points such that they can be considered two separate points in a given microscope under specific experimental parameters. ISBN 081946043-5 owl:Class resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000035 lateral resolution interval as angle https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spatial resolution interval that quantifies the minimum angular separation between two points on a plane orthogonal to the light ray, expressed as an angle centered in the lens (Formula: δθ = 1.22 * λ / D). ISBN 081946043-5 owl:Class spatial resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 $δθ = 1.22\cdotλ/D$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000036 lateral resolution interval as length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spatial resolution interval that quantifies the minimum linear separation between two points on a plane orthogonal to the light ray, expressed as the distance from the center of the optical spot (Formula: δr = 0.61 * λ / NA). ISBN 081946043-5 owl:Class spatial resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 $δr = 0.61\cdotλ/NA$ (Abbe formula, derived from the Rayleigh criterion with the Kirchhoff, Debye and paraxial approximation) $= 1.22 λ\cdot(f/\sharp)$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000037 axial resolution interval as length https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spatial resolution interval that quantifies the minimum measurable separation between two points along the axis of propagation of the light ray, expressed as a linear distance (Formula: δz = 2 ⋅ n ⋅ λ / NA²). ISBN 081946043-5 owl:Class spatial resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 $δz = 2\cdot n\cdotλ/NA²$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000038 spectral resolution interval https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A resolution interval that quantifies the minimum separation between two narrow peaks in a spectrum such that they can be distinguished as two separate peaks. ISBN 081946043-5 owl:Class resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000039 spectral resolution interval as wavelength https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spectral resolution interval that quantifies the minimum separation between two wavelengths such that they can be distinguished as different (Formula: δλ = λ / (n * N)). https://wiki.charisma.ideaconsult.net/wiki/Item:Q22|https://wiki.charisma.ideaconsult.net/wiki/Item:Q200|ISBN 081946043-5 owl:Class spectral resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 $δλ = λ / (n\cdot N) = RF\cdot Δλ\cdot WS / n$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000040 spectral resolution interval as wavenumber https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spectral resolution interval that quantifies the minimum separation between two wavenumbers such that they can be distinguished as different (Formula: δν~ = δλ / λ²). ISBN 081946043-5 owl:Class spectral resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 $δ\barν$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000041 spectral resolution interval as frequency https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spectral resolution interval that quantifies the minimum separation between two frequencies such that they can be distinguished as different (Formula: δν = c * δν~ = c * δλ / λ²). ISBN 081946043-5 owl:Class spectral resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 $δν$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000042 spectral resolution interval as energy https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spectral resolution interval that quantifies the minimum separation between two energy levels such that they can be distinguished as different (Formula: δE = h * δν = h * c * δν~ = h * c * δλ / λ²). ISBN 081946043-5 owl:Class spectral resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 $δE$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000043 radiometric resolution interval https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A resolution interval that quantifies the minimum difference in irradiated energy, often coded as gray level in a grayscale or look-up-table (LUT). ISBN 081946043-5 owl:Class resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000044 temporal resolution interval https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A resolution interval that quantifies the temporal separation between two measurements or frames, often expressed as the inverse of the frame rate. In techniques where temporal resolution is not directly derived from frame rate, it quantifies the minimum temporal interval between two resolvable events. ISBN 081946043-5 owl:Class resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 In techniques where the temporal resolution is not given directly from a temporal distance between subsequent measurements (e.g., pulsed time resolved pump-probe techniques), it can be used more properly as defined above This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0000045 diffraction limit https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 A spatial resolution interval that quantifies the theoretical maximum spatial resolution achievable by an optical system, constrained by the diffraction of light. ISO/DIS 18115-3, https://www.iso.org/obp/ui#d25805417e256 owl:Class spatial resolution interval ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 The Abbe diffraction limit, is defined as λ/ (2 NA) in which λ is the wavelength of the illuminating light and NA is the numerical aperture. This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. -obo:VIBSO_0003017 spectral window center https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/88 A setting datum that specifies the middle wavelength/wavenumber of a spectrum, equal to the average of the maximum and minimum of the spectral window range utilized during the acquisition of spectroscopic data. It corresponds to the optimal alignment or centering of the spectrometer to ensure that the most relevant spectral features are captured effectively within the defined acquisition range. owl:Class setting datum|'is_specified_output_of' some 'center calculation data transformation' ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 560 cm^-1 \ No newline at end of file +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 time|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 grating|grating 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 setting datum A setting datum that specifies the upper boundary of the spectral window range utilized during the acquisition of spectroscopic data. 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 setting datum A setting datum that specifies the lower boundary of the spectral window range utilized during the acquisition of spectroscopic data. 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 = (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 resolution physical quality A physical quality of a measurement device that expresses (realizes) the device's capacity to distinguish between two distinct but closely related measurements of the same physical quality or type, often quantified as the smallest detectable difference (resolution interval) between measured values. This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000032 resolution interval data item|'is about' some resolution|'has value specification' some 'value specification' A data item that quantifies a resolution, by representing the minimum measurable difference between two measurements of the same physical quality or type, such that the measurements can be distinguished as different. This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000033 resolution power ratio A ratio that quantifies the ability of a measurement device to distinguish between small differences in measurement values, expressed as the ratio between a typical measurement datum and the corresponding resolution interval. ISBN 081946043-5 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000034 spatial resolution interval resolution interval A resolution interval that quantifies the minimum distance between two points such that they can be considered two separate points in a given microscope under specific experimental parameters. ISBN 081946043-5 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000035 lateral resolution interval as angle spatial resolution interval A spatial resolution interval that quantifies the minimum angular separation between two points on a plane orthogonal to the light ray, expressed as an angle centered in the lens (Formula: δθ = 1.22 * λ / D). ISBN 081946043-5 $δθ = 1.22\cdotλ/D$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000036 lateral resolution interval as length spatial resolution interval A spatial resolution interval that quantifies the minimum linear separation between two points on a plane orthogonal to the light ray, expressed as the distance from the center of the optical spot (Formula: δr = 0.61 * λ / NA). ISBN 081946043-5 $δr = 0.61\cdotλ/NA$ (Abbe formula, derived from the Rayleigh criterion with the Kirchhoff, Debye and paraxial approximation) $= 1.22 λ\cdot(f/\sharp)$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000037 axial resolution interval as length spatial resolution interval A spatial resolution interval that quantifies the minimum measurable separation between two points along the axis of propagation of the light ray, expressed as a linear distance (Formula: δz = 2 ⋅ n ⋅ λ / NA²). ISBN 081946043-5 $δz = 2\cdot n\cdotλ/NA²$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000038 spectral resolution interval resolution interval A resolution interval that quantifies the minimum separation between two narrow peaks in a spectrum such that they can be distinguished as two separate peaks. ISBN 081946043-5 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000039 spectral resolution interval as wavelength spectral resolution interval A spectral resolution interval that quantifies the minimum separation between two wavelengths such that they can be distinguished as different (Formula: δλ = λ / (n * N)). https://wiki.charisma.ideaconsult.net/wiki/Item:Q22|https://wiki.charisma.ideaconsult.net/wiki/Item:Q200|ISBN 081946043-5 $δλ = λ / (n\cdot N) = RF\cdot Δλ\cdot WS / n$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000040 spectral resolution interval as wavenumber spectral resolution interval A spectral resolution interval that quantifies the minimum separation between two wavenumbers such that they can be distinguished as different (Formula: δν~ = δλ / λ²). ISBN 081946043-5 $δ\barν$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000041 spectral resolution interval as frequency spectral resolution interval A spectral resolution interval that quantifies the minimum separation between two frequencies such that they can be distinguished as different (Formula: δν = c * δν~ = c * δλ / λ²). ISBN 081946043-5 $δν$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000042 spectral resolution interval as energy spectral resolution interval A spectral resolution interval that quantifies the minimum separation between two energy levels such that they can be distinguished as different (Formula: δE = h * δν = h * c * δν~ = h * c * δλ / λ²). ISBN 081946043-5 $δE$ This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000043 radiometric resolution interval resolution interval A resolution interval that quantifies the minimum difference in irradiated energy, often coded as gray level in a grayscale or look-up-table (LUT). ISBN 081946043-5 This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000044 temporal resolution interval resolution interval A resolution interval that quantifies the temporal separation between two measurements or frames, often expressed as the inverse of the frame rate. In techniques where temporal resolution is not directly derived from frame rate, it quantifies the minimum temporal interval between two resolvable events. ISBN 081946043-5 In techniques where the temporal resolution is not given directly from a temporal distance between subsequent measurements (e.g., pulsed time resolved pump-probe techniques), it can be used more properly as defined above This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0000045 diffraction limit spatial resolution interval A spatial resolution interval that quantifies the theoretical maximum spatial resolution achievable by an optical system, constrained by the diffraction of light. ISO/DIS 18115-3, https://www.iso.org/obp/ui#d25805417e256 The Abbe diffraction limit, is defined as λ/ (2 NA) in which λ is the wavelength of the illuminating light and NA is the numerical aperture. This class is actually to general for VIBSO's scope. It needs to be discussed with CHMO and OBI devs which of these is a better home, as there currently does not exist an optical device ontology within OBO Foundry. OBI contains most terms around optical devices so far. ORCID:0000-0003-2673-366X|ORCID:0000-0003-2673-366X|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/125 owl:Class +obo:VIBSO_0003017 spectral window center setting datum|'is_specified_output_of' some 'center calculation data transformation' A setting datum that specifies the middle wavelength/wavenumber of a spectrum, equal to the average of the maximum and minimum of the spectral window range utilized during the acquisition of spectroscopic data. It corresponds to the optimal alignment or centering of the spectrometer to ensure that the most relevant spectral features are captured effectively within the defined acquisition range. 560 cm^-1 ORCID:0000-0002-1595-3213|ORCID:0000-0002-2239-3955 https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/88 owl:Class diff --git a/src/templates/vibso_examples.tsv b/src/templates/vibso_examples.tsv index 7094e0b..b454129 100644 --- a/src/templates/vibso_examples.tsv +++ b/src/templates/vibso_examples.tsv @@ -1,11 +1,11 @@ id label description type executes method achieves objective has specified input has specified output quality of has part is about is concretized as has value specification specifies value of has specified value unit of measure ID AL rdfs:label@en AL dcterms:description@en TYPE I executes I achieves_planned_objective I has_specified_input SPLIT=, I has_specified_output SPLIT=, I quality of I has part SPLIT=, I is about SPLIT=, I is concretized as I has value specification I specifies value of I has specified value I has measurement unit label -ex:_Raman_Spectroscopy_1 _Raman_Spectroscopy_1 The Raman spectroscopy in which _Sample_1 is being assayed according to _Raman_Spectroscopy_Method_1 in order to achieve _Raman_Spectrum_Objective_1. Raman spectroscopy _Raman_Spectroscopy_Method_1 _Raman_Spectrum_Objective_1 _Wavelength_Setting_Info_1,_Sample_1,_Raman_Spectrometer_1 _Raman_Spectrum_1 -ex:_Raman_Spectroscopy_Method_1 _Raman_Spectroscopy_Method_1 The information that indicates the type of _Raman_Spectroscopy_1 by describing its method, specifying its inputs and outputs, as well as the necessary steps and actions that have to be taken in order to achieve _Raman_Spectrum_Objective_1. For the sake of keeping it simple, not all parts of this assay specification will be provided as assertions on this example. investigation assay specification _Raman_Spectrum_Objective_1,_Wavelength_Setting_Info_1 _Raman_Spectroscopy_1,_Raman_Spectrometer_1 -ex:_Raman_Spectrum_Objective_1 _Raman_Spectrum_Objective_1 The information that specifies the intended outcome of _Raman_Spectroscopy_1 to be the creation of a Raman Spectrum. assay objective -ex:_Wavelength_Setting_Info_1 _Wavelength_Setting_Info_1 The information that determines the wavelength of the laser of _Raman_Spectrometer_1 which is used to excite the sample. This information gets encoded by the _Laser_Value_Specification_1. excitation wavelength setting _Laser_Wavelength_1 _Wavelength_Value_Specification_1 -ex:_Laser_Wavelength_1 _Laser_Wavelength_1 The laser wavelength of _Raman_Spectrometer_1 which is a general attribute (aka quality/characteristic) of _Raman_Spectrometer_1. The quantity of this attribute is represented by the _Wavelength_Value_Specification_1. wavelength _Raman_Spectrometer_1 +ex:_Raman_Spectroscopy_1 _Raman_Spectroscopy_1 The Raman spectroscopy in which _Sample_1 is being assayed according to _Raman_Spectroscopy_Method_1 in order to achieve _Raman_Spectrum_Objective_1. Raman spectroscopy _Raman_Spectroscopy_Method_1 _Raman_Spectrum_Objective_1 _Wavelength_Setting_Info_1,_Sample_1,_Raman_Spectrometer_1 _Raman_Spectrum_1 +ex:_Raman_Spectroscopy_Method_1 _Raman_Spectroscopy_Method_1 The information that indicates the type of _Raman_Spectroscopy_1 by describing its method, specifying its inputs and outputs, as well as the necessary steps and actions that have to be taken in order to achieve _Raman_Spectrum_Objective_1. For the sake of keeping it simple, not all parts of this assay specification will be provided as assertions on this example. investigation assay specification _Raman_Spectrum_Objective_1,_Wavelength_Setting_Info_1 _Raman_Spectroscopy_1,_Raman_Spectrometer_1 +ex:_Raman_Spectrum_Objective_1 _Raman_Spectrum_Objective_1 The information that specifies the intended outcome of _Raman_Spectroscopy_1 to be the creation of a Raman Spectrum. assay objective +ex:_Wavelength_Setting_Info_1 _Wavelength_Setting_Info_1 The information that determines the wavelength of the laser of _Raman_Spectrometer_1 which is used to excite the sample. This information gets encoded by the _Laser_Value_Specification_1. excitation wavelength setting _Laser_Wavelength_1 _Wavelength_Value_Specification_1 +ex:_Laser_Wavelength_1 _Laser_Wavelength_1 The laser wavelength of _Raman_Spectrometer_1 which is a general attribute (aka quality/characteristic) of _Raman_Spectrometer_1. The quantity of this attribute is represented by the _Wavelength_Value_Specification_1. wavelength _Raman_Spectrometer_1 ex:_Wavelength_Value_Specification_1 _Wavelength_Value_Specification_1 The encoding of the value determined by _Wavelength_Setting_Info_1, which consists of the unit label and the literal value of the laser wavelength of _Raman_Spectrometer_1. scalar value specification _Laser_Wavelength_1 555.00^^xsd:float nanometer -ex:_Sample_1 _Sample_1 The material entity that is being evaluated in _RamanAssay_1. material sample -ex:_Raman_Spectrometer_1 _Raman_Spectrometer_1 The Raman spectrometer that is used in _RamanAssay_1. Raman spectrometer -ex:_Raman_Spectrum_1 _Raman_Spectrum_1 The Raman spectrum (the data outputed by _RamanSpectrometer_1 NOT the plot) of _Sample_1 created by _RamanAssay_1. Currently classified as an IAO:'data item' as a more specific subclass thereof has yet to be minted in VIBSO (see alos: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77) data item _Sample_1 +ex:_Sample_1 _Sample_1 The material entity that is being evaluated in _RamanAssay_1. material sample +ex:_Raman_Spectrometer_1 _Raman_Spectrometer_1 The Raman spectrometer that is used in _RamanAssay_1. Raman spectrometer +ex:_Raman_Spectrum_1 _Raman_Spectrum_1 The Raman spectrum (the data outputed by _RamanSpectrometer_1 NOT the plot) of _Sample_1 created by _RamanAssay_1. Currently classified as an IAO:'data item' as a more specific subclass thereof has yet to be minted in VIBSO (see alos: https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77) data item _Sample_1 diff --git a/src/templates/vibso_object_properties.tsv b/src/templates/vibso_object_properties.tsv index 36d15f0..0e67c23 100644 --- a/src/templates/vibso_object_properties.tsv +++ b/src/templates/vibso_object_properties.tsv @@ -1,2 +1,2 @@ -id label link(s) to issue(s) definition definition source URI type super property inverse property domain range contributor URI example of usage editor note obsoleted obsolescence reason term replaced by -ID AL rdfs:label@en AI rdfs:seeAlso SPLIT=| AL IAO:0000115@en >AI dc11:source TYPE SP % IP % DOMAIN RANGE AI dc11:contributor SPLIT=| AL IAO:0000112@en AL IAO:0000116@en SPLIT=| AI IAO:0000231 AT owl:deprecated^^xsd:boolean AI IAO:0100001 +id label super property inverse property definition definition source URI domain range example of usage editor note obsoleted obsolescence reason term replaced by contributor URI link(s) to issue(s) type +ID AL rdfs:label@en SP % IP % AL IAO:0000115@en >AI dc11:source DOMAIN RANGE AL IAO:0000112@en AL IAO:0000116@en SPLIT=| AI IAO:0000231 AT owl:deprecated^^xsd:boolean AI IAO:0100001 AI dc11:contributor SPLIT=| AI rdfs:seeAlso SPLIT=| TYPE