NFDI4Chem / VibrationalSpectroscopyOntology

WORK IN PROGRESS - The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.
https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/
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[NTR] add Raman Spectroscopy subtypes according to ISO specs #103

Open StroemPhi opened 1 year ago

StroemPhi commented 1 year ago

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: Raman spectroscopy and mapping techniques drawio

Zack-83 commented 10 months ago

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.:

as well as some negative criteria:

unsure:

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]| | |
StroemPhi commented 10 months ago

Thanks @Zack-83, I put it on the agenda for tomorrow to be discussed.

Stefano-Luin commented 10 months ago

Please change "emitted" photon with "exiting" photon (or something similar). Emission usually refers to a single-photon phenomenon in which an excited state decays with emission of a photon.

Zack-83 commented 9 months ago

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

nicocopez commented 8 months ago

Some comments after the call today.