Add "number of accumulations" (#60)

* Adjust VIBSO_0000007 (previously called number of scans) to be the "number of accumulations" setting datum

---------

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

.gitignore

@@ -40,3 +40,4 @@ src/patterns/all_pattern_terms.txt
 pyproject.toml
 poetry.lock
 .idea/*
+src/templates/.~lock.vibso_classes.tsv\#

src/ontology/components/vibso_classes.owl

@@ -23,7 +23,7 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_classes.owl>
-<http://purl.obolibrary.org/obo/vibso/releases/2023-02-08/components/vibso_classes.owl>
+<http://purl.obolibrary.org/obo/vibso/releases/2023-02-09/components/vibso_classes.owl>
 Annotation(rdfs:comment "This component is derived from the 'src/templates/vibso_classes.tsv', which is edited manually by domain experts."^^xsd:string)
 
 Declaration(Class(obo:CHMO_0000823))
@@ -128,16 +128,15 @@ AnnotationAssertion(rdfs:label obo:VIBSO_0000006 "device temperature setting"@en
 AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000006 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/43>)
 SubClassOf(obo:VIBSO_0000006 obo:IAO_0000140)
 
-# Class: obo:VIBSO_0000007 (number of scans setting)
+# Class: obo:VIBSO_0000007 (number of accumulations)
 
-AnnotationAssertion(obo:IAO_0000112 obo:VIBSO_0000007 "The setting entered into a Raman microscope which specifies the desired number of measurements this Raman microscope has to perform to produce an usable Raman spectrum."@en)
-AnnotationAssertion(obo:IAO_0000115 obo:VIBSO_0000007 "A setting datum that specifies the number of iterations performed in a spectroscopic meassurement from which an aggregated assay output is generated."@en)
-AnnotationAssertion(obo:IAO_0000116 obo:VIBSO_0000007 "This class should better be defined in a more general device ontology."@en)
+AnnotationAssertion(obo:IAO_0000115 obo:VIBSO_0000007 "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."@en)
+AnnotationAssertion(obo:IAO_0000116 obo:VIBSO_0000007 "This class might better be defined in a more general device ontology."@en)
+AnnotationAssertion(obo:IAO_0000118 obo:VIBSO_0000007 "number of acquisitions"@en)
 AnnotationAssertion(dc:contributor obo:VIBSO_0000007 <http://orcid.org/0000-0002-1595-3213>)
-AnnotationAssertion(rdfs:label obo:VIBSO_0000007 "number of scans setting"@en)
-AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000007 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/44>)
+AnnotationAssertion(rdfs:label obo:VIBSO_0000007 "number of accumulations"@en)
+AnnotationAssertion(rdfs:seeAlso obo:VIBSO_0000007 <https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30>)
 SubClassOf(obo:VIBSO_0000007 obo:IAO_0000140)
-SubClassOf(obo:VIBSO_0000007 ObjectSomeValuesFrom(obo:BFO_0000050 obo:VIBSO_0000000))
 
 # Class: obo:VIBSO_0000008 (CCD sensor binning read mode setting)
 

src/templates/vibso_classes.tsv

@@ -7,7 +7,7 @@ obo:VIBSO_0000003	preamplifier gain setting		https://github.com/NFDI4Chem/Vibrat
 obo:VIBSO_0000004	horizontal shift speed setting		https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42	A setting datum that specifies the horizontal shift speed in CCD sensors.		owl:Class	setting datum	ORCID:0000-0002-1595-3213		This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.			
 obo:VIBSO_0000005	vertical shift speed setting		https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/42	A setting datum that specifies the vertical shift speed in CCD sensors.		owl:Class	setting datum	ORCID:0000-0002-1595-3213		This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.			
 obo:VIBSO_0000006	device temperature setting		https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/43	A setting datum that specifies the operating temperature of a device.		owl:Class	setting datum	ORCID:0000-0002-1595-3213		This class should better be defined in a more general device ontology.			
-obo:VIBSO_0000007	number of scans setting		https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/44	A setting datum that specifies the number of iterations performed in a spectroscopic meassurement from which an aggregated assay output is generated.		owl:Class	setting datum|('part of' some 'vibrational spectrometer configuration specification')	ORCID:0000-0002-1595-3213	The setting entered into a Raman microscope which specifies the desired number of measurements this Raman microscope has to perform to produce an usable Raman spectrum.	This class should better be defined in a more general device ontology.			
+obo:VIBSO_0000007	number of accumulations	number of acquisitions	https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/30	A setting datum that specifies the desired number of measurements a spectrometer has to perform on the same location, without position change to produce an usable spectrum. This setting datum is relevant to improve the signal to noise ratio.		owl:Class	setting datum	ORCID:0000-0002-1595-3213		This class might better be defined in a more general device ontology.			
 obo:VIBSO_0000008	CCD sensor binning read mode setting		https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/46	A setting datum that specifies the binning read mode of a device with a CCD sensor.		owl:Class	setting datum	ORCID:0000-0002-1595-3213		This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.			
 obo:VIBSO_0000009	groove density	groove frequency	https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45	A physical quality inhering in a diffraction grating device by virtue of the device's function to diffract light. This quality specifically depends on the number of grooves per area of the grating device and is usually expressed in grooves per millimeter.	Wikipedia:Diffraction_grating|https://www.meetoptics.com/academy/groove-density#:~:text=The%20groove%20density%20(or%20groove,of%20the%20operational%20wavelength%20range	owl:Class	physical quality	ORCID:0000-0002-1595-3213		temp class until NTR in PATO has been accepted and merged (https://github.com/pato-ontology/pato/issues/541)			
 obo:VIBSO_0000010	groove density setting		https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/issues/45	A setting datum that specifies the number of grooves in a diffraction grating device.		owl:Class	setting datum	ORCID:0000-0002-1595-3213		This class should better be defined in a more general device ontology or a domain ontology with the scope of optical devices.