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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[Docs] add section to docs for checking ISO 18115-1/3 in NTR workflow #65

Closed StroemPhi closed 12 months ago

StroemPhi commented 1 year ago

We need to documents as a general workflow that we need:

Zack-83 commented 1 year ago

Here are all terms from Part 3. @RainerStosch proposes to color code them (green/yellow/red) to help deciding what has to be imported into the ontology.

ID Preferred term label Synonyms Textual definition Link to CHARISMA Wiki equivalent Suggested parent term Axiomatization Examples Notes
3.5.1 anti-Stokes Raman scattering def01 3.5.16 [^01]
3.5.2 backscattering configuration def02 optical configuration [^02]
3.5.3 coherent anti-Stokes Raman scattering CARS def03 3.5.1 [^03.1] [^03.2] [^03.3] [^03.4]
3.5.4 coherent Raman scattering microscopy CRS def04 scattering microscopy [^04]
3.5.5 coherent Stokes Raman scattering CSRS def05 3.5.25 [^05.1] [^05.2] [^05.3] [^05.4]
3.5.6 confocal Raman microscopy def06 3.5.17 [^06]
3.5.7 depolarization ratio def07 intensity ratio [^07]
3.5.8 electronic Raman scattering def08 3.5.16 [^08]
3.5.9 enhancement factor def09 intensity ratio [^09.1]; [^09.2]
3.5.10 hyper-Raman scattering def10 inelastic light scattering [^10]
3.5.11 polarized Raman spectroscopy def11 3.5.17 [^11]
3.5.12 Raman amplification def12 intensity ratio [^12]
3.5.13 Raman depth profiling def13 3.5.14 [^13]
3.5.14 Raman mapping Raman imaging def14 mapping [^14]
3.5.15 Raman optical activity ROA def15 optical activity [^15]
3.5.16 Raman scattering Raman effect def16 inelastic light scattering [^16]
3.5.17 Raman spectroscopy def17 optical spectroscopy [^17]
3.5.18 Raman tensor def18 tensor [^18]
3.5.19 Raman shift def19 energy difference [^19]
3.5.20 resonance Raman spectroscopy RR def20 3.5.17 [^20]
3.5.21 rotational Raman spectroscopy def21 3.5.17 [^21]
3.5.22 spontaneous Raman spectroscopy def22 3.5.17 [^22]
3.5.23 spatially offset Raman spectroscopy SORS def23 3.5.17 [^23]
3.5.24 stimulated Raman scattering SRS def24 3.5.16 [^24.1] [^24.2]
3.5.25 Stokes Raman scattering def25 3.5.16 [^25]
3.5.26 surface-enhanced Raman spectroscopy SERS def26 3.5.17 [^26]
3.5.27 surface-enhanced Raman scattering SERS def27 3.5.16 [^27.1] [^27.2] [^27.3]
3.5.28 surface-enhanced resonant Raman scattering SERRS def28 3.5.16 [^28]
3.5.29 surface-enhanced resonant Raman spectroscopy SERRS def29 3.5.20 [^29]
3.5.30 tip-enhanced Raman spectroscopy TERS def30 3.5.20 [^30]
3.5.31 tip-enhanced resonance Raman spectroscopy TERRS def31 3.5.20 [^31]
3.5.32 transmission Raman spectroscopy def32 3.5.17 [^32]
3.5.33 resonant excitation profile def33 [^33]
3.5.34 transmission configuration def34 optical configuration [^34]
3.5.35 vibrational-rotational spectroscopy def35 optical spectroscopy [^35]

[^01]: [^02]: Note 1 to entry: This is the typical configuration of a Raman spectrometer coupled with a microscope. [^03.1]: Note 1 to entry: CARS signal is generated in samples due to third-order nonlinear susceptibility and requires three laser beams. A Stokes beam with frequency ωs, a pump beam with frequency ωp and a probe beam with frequency ωpr. When the photons of the beams interact, they produce an anti-Stokes frequency (ωpr +ωp −ωs), when the term (ωp −ωs) matches the vibrational frequency of the Raman resonance then the anti-Stokes frequency is enhanced producing an orders stronger Raman signal comparing to spontaneous Raman spectroscopy. [^03.2]: Note 2 to entry: See also anti-Stokes Raman scattering (3.5.1). [^03.3]: Note 3 to entry: It is a third order process as it is the cubic component of the Taylor series expansion of the nonlinear susceptibility. [^03.4]: Note 4 to entry: coherent -Stokes Raman scattering (CSRS) (3.5.5) is the opposite of CARS. [^04]: Note 1 to entry: Under the family of CRS are the techniques of coherent anti-Stokes Raman scattering (CARS) (3.5.3), CSRS (3.5.5) and stimulated Raman scattering (SRS) (3.5.24). [^05.1]: Note 1 to entry: CSRS requires three laser beams, the anti-Stokes beam with frequency ωAs, a pump beam with frequency ωp and a probe beam with frequency ωpr. When the photons of the beams interact they produce a Stokes frequency (ωpr +ωp −ωΑs), w hen t he t erm (ωp −ωΑs) matches the vibrational frequency of the Raman resonance then the Stokes frequency is enhanced producing an orders stronger Raman signal comparing to spontaneous Raman spectroscopy. [^05.2]: Note 2 to entry: See also Stokes Raman scattering (3.5.25). [^05.3]: Note 3 to entry: It is a third order process as it is the cubic component of the Taylor series expansion of the nonlinear susceptibility. [^05.4]: Note 4 to entry: CSRS is pronounced as “scissors”. [^06]: [^07]: [^08]: [^09.1]: Note 1 to entry: The enhancement factor is the product of the contrast and the ratio of the volumes analysed without the probe and with the probe. [^09.2]: Note 2 to entry: In TERS the enhancement is due to the presence of the probe and in SERS it is due to the presence of a surface that is typically metallic and contains nanoscale features. [^10]: [^11]: Note 1 to entry: This is typically achieved using combinations of retardation plates (3.1.34), scrambler and polarizers (3.1.28) in the optical path. [^12]: Note 1 to entry: See CARS (3.5.3) and SRS (3.5.24) as examples of Raman amplification. [^13]: [SOURCE: adapted from ISO 14606:2015, 3.6] [^14]: Note 1 to entry: Raman spectral mapping and Raman spectral imaging are terms that are also used. [^15]: Note 1 to entry: The method probes biomolecular structure and behaviour in aqueous liquids. [^16]: Note 1 to entry: Typically, monochromatic optical radiation is used to probe vibrational or rotational energy levels in a molecular or crystalline sample. [^17]: [SOURCE: ISO/TS 80004‑13:2017, 3.3.1.6, modified replaced emitted by scattered] [^18]: [^19]: Note 1 to entry: Raman shift is typically expressed in wavenumbers. [^20]: [^21]: [^22]: Note 1 to entry: There is no enhancement of sensitivity. This is in contrast to stimulated Raman scattering (3.5.24). [^23]: Note 1 to entry: The method is used for chemical analysis at a sub-surface level for example inside biological material or inside packaging. [^24.1]: Note 1 to entry: The difference frequency sometimes called as “beat frequency”. [^24.2]: Note 2 to entry: The SRS signal strength is linearly proportional to the concentration. [^25]: Note 1 to entry: See anti-Stokes Raman scattering (3.5.1). [^26]: Note 1 to entry: The acronym SERS is used for both surface-enhanced Raman scattering and spectroscopy. [^27.1]: Note 1 to entry: The acronym SERS is used for both surface-enhanced Raman scattering and spectroscopy. [^27.2]: Note 2 to entry: The enhancement is particularly strong for gold and silver surfaces of appropriate surface roughness, when excited by a laser at the correct wavelength. [^27.3]: Note 3 to entry: Surface-enhanced Raman scattering is utilized via a tip-enhancement in TERS (3.5.30). [^28]: Note 1 to entry: The acronym SERRS is used for both surface-enhanced resonant Raman scattering and spectroscopy. [^29]: Note 1 to entry: The acronym SERRS is used for both surface-enhanced resonant Raman scattering and spectroscopy. [^30]: Note 1 to entry: TERS provides higher scattering cross-section and higher spatial resolution than confocal Raman microscopy. [^31]: [^32]: Note 1 to entry: This can be used for samples up to approximately 10 mm thick with the collected Raman signal representative of the bulk material. The thickness depends on the transmittance of the sample to the excitation light. [^33]: [^34]: Note 1 to entry: Compare with backscattering configuration (3.5.2). [^35]: Note 1 to entry: Raman and Infrared spectroscopy are the main representative techniques of this family, each technique being sensitive to different type of vibrations and provide complementary vibrational spectra.

"Attribution"

ORCID:0000-0002-1595-3213|ORCID:0000-0001-7694-5519|ORCID:0000-0002-2239-3955

StroemPhi commented 12 months ago

closed in favor of #96