Add resolution-related terms and definitions (#134)

* Add new terms to src/templates/vibso_classes.tsv
* add diffraction limit
* Subsuming 'resolution' under PATO:'physical quality' and improving the definition to be more in line with the Genus+Differentia structure.
* Subsume 'resolution interval' under IAO:'data item' and sharpen its definition.
* Subsume 'resolution power' under STATO:'ratio' and sharpen its definition
* Refine definition of 'spatial resolution interval' classes according to Genus + Differentia structure
* Refine definitions of 'spectral resolution interval' classes according to Genus + Differentia structure
* Iprove definitions to be in line with the others in their Genus + Differentia structure.
* Sharpening the definition of 'resolution interval' by connecting it to 'resolution' also adding subclassOf axioms to reflect this
* Updating the TBox graphic with the newly added classes
* adjust formulae and wording
* Add editor note about out-of-scope todo for all the resolution terms
* Add links to CHARISMA SMW
* Fixing term contributor ORCID

---------

Co-authored-by: Philip Strömert <Philip.Stroemert@tib.eu>

src/ontology/vibso-edit.owl

@@ -42,6 +42,7 @@ Annotation(dcterms:description "_WIP - NOT READY FOR PRODUCTION_ The Vibration S
 Annotation(dcterms:license <https://creativecommons.org/licenses/by/4.0/>)
 Annotation(dcterms:title "Vibrational Spectroscopy Ontology")
 
+Declaration(NamedIndividual(<http://orcid.org/0000-0003-2673-366X>))
 Declaration(NamedIndividual(ex:AssayObjective_O))
 Declaration(NamedIndividual(ex:Assay_A))
 Declaration(NamedIndividual(ex:DataItem_D))
@@ -128,6 +129,13 @@ SubClassOf(obo:UO_0000051 obo:IAO_0000003)
 #   Named Individuals
 ############################
 
+# Individual: <http://orcid.org/0000-0003-2673-366X> (Stefano Luin)
+
+AnnotationAssertion(rdfs:label <http://orcid.org/0000-0003-2673-366X> "Stefano Luin")
+AnnotationAssertion(<https://schema.org/affiliation> <https://orcid.org/0000-0001-7694-5519> "VIBSO Working Group"@en)
+ClassAssertion(obo:NCBITaxon_9606 <http://orcid.org/0000-0003-2673-366X>)
+
+
 # Individual: ex:AssayObjective_O (ex:AssayObjective_O)
 
 ClassAssertion(obo:OBI_0000441 ex:AssayObjective_O)

src/templates/vibso_classes.tsv

@@ -28,6 +28,22 @@ 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	Raman raw data	raw Raman data	https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/77	A measurment 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_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. 			
+