[NTR] add Raman Spectroscopy subtypes according to ISO specs

[StroemPhi]

This issue addresses the need to have classes in VIBSO that represent the various Raman spectroscopy assay types defined in the ISO18115:3 specs.

How we will do this is described in the below comment by@Zack-83.

In Raman.methods.ISO.CHMO.CHARISMA.xlsx we edit the proposed definitions, the priority of which terms from our sources to include, what superclasses they have and other information about them. If you want to add a comment or propose a change in it, please download the most current version attached here and add then upload your version in a new comment below.

A visual overview is also offered:

[Zack-83]

Our authoritative sources: CHMO, ISO18115:3 and CHARISMA, contain an overview of Raman sub-techniques (assays).

Neither of these is complete nor strictly coherent. Therefore it is our task to establish a classification of techniques and include it into VIBSO (or propose it to CHMO).

To put order within the jungle, we need to define some positive criteria, e.g.:

• techniques defined by a distinctive adjective (e.g. coherent vs non-coherent)
• techniques defined by an established combination of two or more adjectives (e.g. SERS, CARS)
• techniques which imply a specific set of experimental parameter

as well as some negative criteria:

• techniques defined by a casual combination of two or more adjectives (e.g. deep ultra-violet resonance Raman spectroscopy)
• techniques described in relation to aspects independent from the acquisition method such as sample preparation (e.g. drop coating deposition Raman spectroscopy)

unsure:

• techniques whose denomination does not differentiate it from the default (e.g. laser Raman spectroscopy: nowadays no experiment is conducted without a laser)
• techniques who do not imply different parameters (e.g. infrared vs ultra-violet vs visible)
• techniques which are too seldom, old or restricted (e.g. transmission Raman spectroscoy)

The combination techniques should be included axiomatically, by allowing instances to belong to more classes:

# An example of surface-enhanced anti-Stokes confocal Raman spectroscopy
ex:Measurement1 rdf:type vibso:RamanSpec_SurfaceEnhanced , # implies parameters about the surface
                         vibso:RamanSpec_AntiStokes ,      # implies a restriction on Raman shifts <0
                         vibso:RamanSpec_Confocal .        # implies parameters on the focal depth...

Terms to add

ID	label	alternative term	definition	notes	parent element
ISO18115:3.5.16	Raman scattering	Raman effect	def16	16	inelastic light scattering
CHMO:0000656; ISO18115:3.5.17; CHARISMA:Q87	Raman spectroscopy		def17	17	optical spectroscopy ∩ scattering spectroscopy (< assay)
	Raman microscopy				optical microscopy (< assay)
CHMO:0000663	confocal Raman spectroscopy				Raman spectroscopy
CHMO:0000664; ISO18115:3.5.06	confocal Raman microscopy		def06		Raman microscopy
CHMO:0001986	non-resonance Raman spectroscopy				Raman spectroscopy
CHMO:0000668; ISO18115:3.5.20; CHARISMA:Q234	resonance Raman spectroscopy	RR	def20		Raman spectroscopy
CHMO:0000677; ISO18115:3.5.26	surface-enhanced Raman spectroscopy	SERS	def26	26	Raman spectroscopy
CHMO:0000678; ISO18115:3.5.30	tip-enhanced Raman spectroscopy	TERS	def30	30	Raman spectroscopy
CHMO:0000670; ISO18115:3.5.29	surface-enhanced resonant Raman spectroscopy	SERRS	def29	29	resonance ∩ surface-enhanced Raman spectroscopy
ISO18115:3.5.31	tip-enhanced resonance Raman spectroscopy	TERRS	def31		resonance ∩ tip-enhanced Raman spectroscopy
	Stokes Raman spectroscopy				Raman spectroscopy
	anti-Stokes Raman spectroscopy				Raman spectroscopy
CHMO:0000658	coherent Raman spectroscopy	CRS			Raman spectroscopy
CHMO:0000659	coherent Stokes Raman spectroscopy	CSRS			coherent ∩ Stokes Raman spectroscopy
CHMO:0000661	coherent anti-Stokes Raman spectroscopy	CARS			coherent ∩ anti-Stokes Raman spectroscopy
ISO18115:3.5.22; CHARISMA:Q236	spontaneous Raman spectroscopy		def22	22	Raman spectroscopy
CHMO:0000675; CHARISMA:Q237	stimulated Raman spectroscopy	SRS			Raman spectroscopy
CHMO:0001939	stimulated Raman gain spectroscopy				stimulated Raman spectroscopy
CHMO:0001940	stimulated Raman loss spectroscopy				stimulated Raman spectroscopy
CHMO:0000657	chiral Raman spectroscopy				Raman spectroscopy
ISO18115:3.5.23; CHARISMA:Q235	spatially offset Raman spectroscopy	SORS	def23	23	Raman spectroscopy
CHMO:0000667; ISO18115:3.5.11; CHARISMA:Q117	polarized Raman spectroscopy	polarised Raman spectroscopy	def11	11	Raman spectroscopy

Unsure

ID	label	alternative term	definition	notes	parent element
CHMO:0001766; ISO18115:3.5.32	transmission Raman spectroscopy		def32	32	Raman spectroscopy
ISO18115:3.5.14	Raman mapping	Raman imaging	def14	14	Raman microscopy ∩ mapping technique
ISO18115:3.5.13	Raman depth profiling		def13	13	Raman mapping
ISO18115:3.5.04	coherent Raman scattering microscopy	CRS	def04	04	Raman microscopy ∩ coherent microscopy
ISO18115:3.5.35	vibrational-rotational spectroscopy		def35	35	optical spectroscopy
ISO18115:3.5.21	rotational Raman spectroscopy		def21		Raman spectroscopy
	electronic Raman spectroscopy				Raman spectroscopy
CHMO:0000870	near-infrared Raman spectroscopy				Raman spectroscopy
CHMO:0000680	ultraviolet Raman spectroscopy				Raman spectroscopy
CHMO:0000656	laser Raman spectroscopy				Raman spectroscopy
CHMO:0000666	hyper Raman spectroscopy				Raman spectroscopy OR scattering spectroscopy
	back focal plane imaging	Fourier space imaging, Fourier-plane imaging			Raman spectroscopy

Terms to be dropped

Techniques not fulfilling the criteria:

ID	label
CHMO:0000671	ultraviolet resonance Raman spectroscopy
CHMO:0000672	deep ultra-violet resonance Raman spectroscopy
CHMO:0000662	coherent anti-Stokes resonance Raman spectroscopy
CHMO:0000660	coherent Stokes resonance Raman spectroscopy
CHMO:0000669	Kerr-gated resonance Raman spectroscopy
CHMO:0000885	chiral surface-enhanced Raman spectroscopy
CHMO:0002373	surface-enhanced non-resonance Raman spectroscopy
CHARISMA:Q239	Surface-enhanced spatially offset Raman spectroscopy
CHARISMA:Q238	Surface plasmon polariton enhanced Raman spectroscopy
CHMO:0000875	electrochemical surface-enhanced Raman spectroscopy
CHMO:0000770	single molecule surface-enhanced Raman spectroscopy
CHMO:0000679	ultra-high vacuum tip-enhanced Raman spectroscopy
CHMO:0002165	drop coating deposition Raman spectroscopy
CHMO:0001943	spectral excitation higher-order Raman spectroscopy
CHMO:0001767	optical tweezers Raman spectroscopy
CHMO:0000675	stimulated Raman spectroscopy
CHMO:0001942	ionisation-detected stimulated femtosecond Raman spectroscopy
CHMO:0001941	photoacoustic Raman spectroscopy
CHMO:0000665	Fourier transform Raman spectroscopy

Phenomena listed in ISO18115, converted to techniques:

ID	label	alternative term	definition	notes
ISO18115:3.5.08	electronic Raman scattering		def08
ISO18115:3.5.24	stimulated Raman scattering	SRS	def24	24-1 24-2
ISO18115:3.5.25	Stokes Raman scattering		def25	25
ISO18115:3.5.01	anti-Stokes Raman scattering		def01

Phenomena listed in ISO18115, for which the equivalent technique is already defined:

ID	label	alternative term	definition	notes
ISO18115:3.5.05	coherent Stokes Raman scattering	CSRS	def05	05-1 05-2 05-3 05-4
ISO18115:3.5.03	coherent anti-Stokes Raman scattering	CARS	def03	03-1 03-2 03-3 03-4
ISO18115:3.5.27	surface-enhanced Raman scattering	SERS	def27	27-1 27-2 27-3
ISO18115:3.5.28	surface-enhanced resonant Raman scattering	SERRS	def28	28
ISO18115:3.5.10	hyper-Raman scattering		def10

Other terms which do not describe a technique (to be moved to another issue)

Configurations:

ID	label	alternative term	definition	notes	parent element
ISO18115:3.5.02	backscattering configuration		def02	02	optical configuration
ISO18115:3.5.34	transmission configuration		def34	34	optical configuration

Parameters/quantities:

ID	label	alternative term	definition	notes	parent element
ISO18115:3.5.19	Raman shift		def19	19	energy difference
ISO18115:3.5.07	depolarization ratio		def07		intensity ratio
ISO18115:3.5.09	enhancement factor		def09	09-1 09-2	intensity ratio
ISO18115:3.5.12	Raman amplification		def12	12	intensity ratio
ISO18115:3.5.15	Raman optical activity	ROA	def15	15	optical activity
ISO18115:3.5.18	Raman tensor		def18		tensor
ISO18115:3.5.33	resonant excitation profile		def33

[Zack-83]

As discussed, we prefer to define the full hierarchy tree starting from "Raman spectroscopy" (an assay) rather than "Raman scattering" (a phenomenon)

[nicocopez]

Some comments after the call today.

• TERS is related to the setup. The tip which is used as enhancer is connected to a feedback system to control is position and it is indepentent of the sample. SERS can be part of the sample (for example, the molecules to be tested can be synthesized on the surface of nanoparticle or a substrate). However, one can also just drop molecules on top of a SERS substrate (to me, this would be more in the direction of "setup" classification).
• SERS/TERS are types of enhanced spectroscopy but they can also be called near-field (enhanced) spectroscopies or antenna-enhanced spectroscopies.
• I would include wide-field microscopy in contraposition to confocal microscopy.
  Not sure if here is the right place to mention this. So please correct me if I am wrong.