Add terms defined in Parameters_and_Units_IR_and_Raman_for_VIBSO.xlsx

[StroemPhi]

Lars Meyer (BASF) was so kind to provide Parameters_and_Units_IR_and_Raman_for_VIBSO.xlsx in which he provided a list of parameters and their unist that are relevant in IR and Raman spectroscopy. We thus need to check which of these we already have, need to mint or import.

[StroemPhi]

I went over the terms listed in the XLSX and checked if they are already in VIBSO and/or the CHARISMA wiki.

Terms that are already in VIBSO or have an existing issues:

needed term	VIBSO term or issue	CHARISMA link	comments
Magnification	objective magnification factor setting		add synonyms magnification and maybe magnification #setting, no CHARISMA term yet
Wavelength	PATO:wavelength	Wavelength	unclear what this is needed for, if we there is a wavelenght measured somewhere, we need a measuremtn datum for it
Grating	groove density setting		add synonyms grating and grating setting
Integration time	integration time setting	???Integration period???	add synonym integration time
Instrument	spectrometer & manufacturer	Spectrometer & Spectrograph
Laser (wavelength of laser)	excitation wavelength setting	Laser wavelength	add better synonyms?
Laser power	incident light power datum	Laser power
Number of acumulations	number of accumulations
Method			unclear if this refers to the mapping mode discussed in #28 or to the various existig subclasses of laser Raman spectroscopy
Sampling accessory	diffraction grating, microscope, spectrometer, Raman spectrometer, Raman microscope		Other devices need to be defined yet in NTRs. Which are really necessary from a POV centered around finding the right dataset, not reproducing the research?
gain	preamplifier gain setting

Terms that already exist but not in VIBSO yet need to be imported from external ontologies:

needed term	existing external term	CHARISMA link	comments
concentration quality	PATO:concentration of	Concentration
Model	iao:model number		to be able to further denote the specific kind of spectrometer used, if the chmo:spectrometer class might not suffice for this
Mass (weight of sample, solvent, reagent, etc.)	IAO:mass measurement datum	----	----
Solvent	OBI:solvent role		Chemicals that are used as solvents will have this solvent role in RDF
Density	pato:mass density

Terms needed to be minted in VIBSO or requested in external ontologies:

needed term	possible parent	CHARISMA link	definition	comments
Absorbance	need to adapt absorbance placed under iao:measurement datum	Absorbance ?	https://doi.org/10.1351/goldbook	#86
Absorbance maximum or Peak position	IAO:scalar measurement datum	Absorption band		#89
concentration	actually it is CHMO:concentration, but it should be a IAO:scalar measurement datum	concentration		#90
Pathlength	a length measurement datum	Sample pathlength	Thickness of layer, film, cuvette, deposit --> IR or Raman, if latter difference to region of interest depth needs to be made clear if there is any
Content (Amount of any type per mass of liquid or gas or solid system)			https://doi.org/10.1351/goldbook
Particle area	iao:scalar measurement datum		area of particles in IR/Raman microscopy relative to total area	do we need the total illuminated surface area of the sample then as well? And is this related to https://pubmed.ncbi.nlm.nih.gov/27671141/?
Scans (number of scans used to measure a spectrum)	need to adapt from nmrCV:number of scans		is related to discussion in #30
Particle count	iao:count		number of counted particles in IR/Raman microscopy
Peak Area	measurement datum --> adapt afo:peak area
Peak Height (measurement datum)	measurement datum --> adapt afo:peak height		absolute Peak Height
Raman Intensity	measurement datum --> adapt from AFO:Raman Intensity
Raman shift	measurement datum --> adapt from Raman wavenumber shift
Reflectance	measurement datum --> adapt from reflectance
relative Peak Area	measurement datum --> adapt from relative peak area
relative Peak Height	measurement datum --> adapt from relative peak height
Wavenumber	measurement datum --> adapt from wavenumber	Wavenumber
viscosity value	measurement datum of pato:viscosity --> adapt afo:viscosity
resolution	setting datum --> adapt from resolution
Hydroxyl value	measurement datum		In analytical chemistry, the hydroxyl value is defined as the number of milligrams of potassium hydroxide (KOH) required to neutralize the acetic acid taken up on acetylation of one gram of a chemical substance that contains free hydroxyl groups.
acid value	measurement datum		In chemistry, acid value (AV, acid number, neutralization number or acidity) is a number used to quantify the acidity of a given chemical substance. It is the quantity of base (usually potassium hydroxide (KOH)), expressed as milligrams of KOH required to neutralize the acidic constituents in 1 gram of a sample.
Content of water in sample	a measurement datum
content of active ingredient	a measurement datum			ppm
calculated content AI	a content of active ingredient
average content AI	a content of active ingredient
dilution factor	a data item adapt from afo:dilution factor
refractive index	a data item adapt from cheminf:refractive index descriptor			CHEMINF hs issues preventing it from being imported directly
Pressure	a data item adapt from cheminf:vapour pressure descriptor		A iao:scalar measurement datum or setting datum that is about a PATO:pressure Are we talking about a setting or measurement?	CHEMINF has issues preventing it from being imported directly
pH value	a data item adapt from proco:solution pH datum or cheminf:pH descriptor		needed axiomatization CHMO:pH measurement of PATO:acidity

• date & time of the measurement --> assuming this refers to the date/time a Raman record or a part thereof was created, we'd use standard terms from the Dublin Core ontology like DC:created or DC:date

Terms mentioned in the XLSX that remain unclear and need to be discussed/described further:

• Kubelka Munk
• Identity (Identity of Sample)
• First derivative
• Second derivative
• Log (1/R)
• Quotient (e.g. Relative peak/area heights)
• number of scans used to measure a spectrum --> difference to number of accumulations = creation of mean spectrum?

[StroemPhi]

Any help from others for making NTR issues for the terms listed in the third table is highly welcome.

[StroemPhi]

accidentally closed this with #100