Add absorbance (DO NOT MERGE YET)

src/ontology/components/vibso_classes.owl

@@ -24,8 +24,8 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_classes.owl>
-<http://purl.obolibrary.org/obo/vibso/releases/2024-08-09/components/vibso_classes.owl>
-Annotation(rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_classes.tsv' template.")
+<http://purl.obolibrary.org/obo/vibso/releases/2023-06-23/components/vibso_classes.owl>
+Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_classes.tsv', which is edited manually by domain experts.")
 
 Declaration(Class(obo:BFO_0000029))
 Declaration(Class(obo:CHMO_0000823))
@@ -37,6 +37,7 @@ Declaration(Class(obo:OBI_0000654))
 Declaration(Class(obo:OBI_0000968))
 Declaration(Class(obo:OBI_0200000))
 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))
@@ -69,6 +70,7 @@ Declaration(Class(obo:VIBSO_0000028))
 Declaration(Class(obo:VIBSO_0000029))
 Declaration(Class(obo:VIBSO_0000030))
 Declaration(ObjectProperty(obo:BFO_0000050))
+Declaration(ObjectProperty(obo:IAO_0000136))
 Declaration(ObjectProperty(obo:OBI_0000293))
 Declaration(ObjectProperty(obo:OBI_0000312))
 Declaration(AnnotationProperty(obo:IAO_0000112))
@@ -404,9 +406,12 @@ AnnotationAssertion(rdfs:label obo:VIBSO_0000027 "number of measurements Z"@en)
 AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000027 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/32>)
 SubClassOf(obo:VIBSO_0000027 obo:IAO_0000140)
 
+
+# Class: obo:VIBSO_0000028 (absorbance)
+
 # Class: obo:VIBSO_0000028 (Raman raw data)
 
-AnnotationAssertion(Annotation(dc:source <https://wiki.charisma.ideaconsult.net/wiki/Item:Q64>) obo:IAO_0000115 obo:VIBSO_0000028 "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."@en)
+AnnotationAssertion(Annotation(dc:source <https://wiki.charisma.ideaconsult.net/wiki/Item:Q64>) obo:IAO_0000115 obo:VIBSO_0000028 "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."@en)
 AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000028 "raw Raman data"@en)
 AnnotationAssertion(dc:contributor obo:VIBSO_0000028 <http://orcid.org/0000-0002-2239-3955>)
 AnnotationAssertion(rdfs:label obo:VIBSO_0000028 "Raman raw data"@en)
@@ -435,5 +440,13 @@ AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000030 <https://github.com/NFDI4Chem
 SubClassOf(obo:VIBSO_0000030 obo:IAO_0000027)
 SubClassOf(obo:VIBSO_0000030 ObjectSomeValuesFrom(obo:OBI_0000312 ObjectIntersectionOf(obo:OBI_0200000 ObjectSomeValuesFrom(obo:OBI_0000293 obo:VIBSO_0000028))))
 
+AnnotationAssertion(Annotation(dc:source <http://purl.allotrope.org/ontologies/result#AFR_0001157>) Annotation(dc:source <https://doi.org/10.1351/goldbook>) 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 <http://orcid.org/0000-0002-1595-3213>)
+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 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/86>)
+SubClassOf(obo:VIBSO_0000028 obo:IAO_0000027)
+SubClassOf(obo:VIBSO_0000028 ObjectSomeValuesFrom(obo:IAO_0000136 obo:PATO_0001293))
+
 
-)
+)

src/ontology/components/vibso_object_properties.owl

@@ -24,9 +24,6 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_object_properties.owl>
-<http://purl.obolibrary.org/obo/vibso/releases/2024-01-31/components/vibso_object_properties.owl>
-Annotation(rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_object_properties.tsv' template.")
-
-
-
-)
+<http://purl.obolibrary.org/obo/vibso/releases/2023-06-22/components/vibso_object_properties.owl>
+Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_object_properties.tsv', which is edited manually by domain experts.")
+)

src/templates/vibso_classes.tsv

@@ -2,15 +2,15 @@ id	label	alternative term	link(s) to issue(s)	definition	definition source URI	t
 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_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	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.			
@@ -26,8 +26,9 @@ obo:VIBSO_0000022	point distance X	sampling pace in the X direction|sampling ste
 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_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 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	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