[NTR] add "Raman spatial dimensionality"

[Zack-83]

Preferred term label	Synonyms	Textual definition	Link to CHARISMA Wiki equivalent	Suggested parent term	Axiomatization	Examples	Attribution
Raman mapping specification	Raman imaging specification; Raman acquisition specification	A plan specification...		IAO:plan specification
Raman single-point mapping specification		A Raman mapping specification in which...		Raman mapping specification
Raman point-by-point mapping specification		A Raman mapping specification in which...		Raman mapping specification
Raman line-focus mapping specification		A Raman mapping specification in which...		Raman mapping specification
Raman mapping	Raman imaging; Raman spectral mapping; Raman spectral imaging	An assay implementing a mapping specification...		OBI:assay
Raman map		An image produced via a Raman mapping...
Raman 0D map		A Raman map defined by one single point.		Raman map
Raman horizontal 1D map				Raman map
Raman vertical 1D map				Raman map
Raman horizontal 2D map				Raman map
Raman vertical 2D map				Raman map
Raman 3D map				Raman map

Attribution

ORCID:0000-0001-7694-5519; ORCID:0000-0002-2239-3955

[StroemPhi]

@Zack-83 can you please provide more context as to what you mean with this exactly, maybe links to papers? Also have you checked in the Raman spectroscopy branch we import from CHMO in VIBSO, if these "methods" are defined there as special kinds of Raman spectroscopy? For me the question would be if you are refering to a specialization/kind of Raman spectroscopy or to a special kind of output generated by a certain Raman spectroscopy, so focusing on the generated spectrum.

[StroemPhi]

If you refer to the former, a special kind of Raman spectroscopy, we would have to create new subclasses of either chmo:Raman spectroscopyor chmo:laser Raman spectroscopy, which is probably similar to chmo:two-dimensional infrared spectroscopy.

[Zack-83]

I checked. It seems the spatial dimension is not considered in CHMO.
I will ask @RainerStosch or @Stefano-Luin if other aspects are relevant to distinguish among techniques

[Zack-83]

We have renamed the class and the admitted values to make it clear, that we are only taking about the spatial component. An alternative label ("Raman scan mode") is also provided (see https://github.com/NFDI4Chem/VibrationalSpectroscopyOntology/blob/main/data_examples/Raman_example_data_PTB/Witec/WITec_control_Screen.PNG).

This spatial information can be registered independently from the subclasses defined in https://terminology.nfdi4chem.de/ts/ontologies/vibso/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000656

Concerning the subclasses, we have two questions: who defined them and with which criteria? That classification mixes up different aspects: source, excitation band, enhancement, sample preparation... At least the sample preparation should not be considered, because it has nothing to do with the analytical method used after that.

We can help sorting the chaos :)

[StroemPhi]

Regarding the existing children of CHMO:Raman spectroscopy, all I can say is that we would have to contact @batchelorc or better file an issue in CHMO directly to find out more about their history. My hope was that we can reuse as many of these subclasses as possible and mint new ones only where this is not possible. And once VIBSO is in a more mature state we would have to speak to Colin and the OBI devs anyway to finally decide where should live what. But I think it is best to have a working proposal with VIBSO that can be constructivly discussed with all necessary ontology stakeholders.

[StroemPhi]

Raman Spectroscopy for Chemical Analysis, p. 294ff
Are you talking about this?

[Zack-83]

Raman Spectroscopy for Chemical Analysis, p. 294ff Are you talking about this?

Yes, our addition goes in the same direction. But we foresee a third dimension z, which produces three more cases (vertical scan, vertical surface, volume)

[StroemPhi]

I've been spending quite some time trying to understand the things requested in this issue. What became clear to me from our previous discussions is that the requested "Raman spatial dimensionality" should be understood as the "method" or chosen protocol which specifies how the sample should be scanned when using a certain kind of Raman spectroscopy, like confocal Raman microscopy. It is thus best subsumed under IAO:plan specification, as this class is used in the definition of OBI planned process (the parent of Raman spectroscopies in VIBSO). Yet I think it is best to not label this class "Raman spatial dimensionality" but instead use the suggested synonym "Raman scan mode" to make more explicit what we are actually talking about. Because what isn't clear to me yet with regard to the dimentionaly is whether it should refer to the dimentions in which the sample was scanned or the dimensions of the resulting Raman image. This becomes apparent when we have for example a 1D line mapping that uses a line focused laser beam. The resulting Raman image of an assay implementing this mode would be 2D. What I'm trying to say, is that for VIBSO we need to break it down more fine grained and should probably define the competency questions we need to describe what we actually want to say with these terms. What I'd like to propose concretely for now are these classes:

• IAO:plan specification

  • Raman imaging mode
    -- synonym: Raman aquisition mode
    -- def.: A plan specifiaction that specifies the spatial coverage of a Raman spectroscopy experiment, by determining whether to produce a Raman image of the region of interest (ROI) from a single scan or instead from multiple mapped scans.

    • Raman single scan mode
      -- def: A Raman scan mode that specifies to scan the region of interest (ROI) at once, by focusing the laser beam to cover the whole ROI.
      -- comment: The spatial resolution of a Raman image produced with this mode is determined by the magnification of the optics in the system and the size of the elements in the detector.
    • Raman mapping mode
      -- def.: A Raman scan mode that specifies to scan the region of interest (ROI) pointwise, by using a steady laser focus smaller than the ROI at different locations on the sample within an equally spaced grid spanning the ROI.
      -- comment: The spatial resolution of a Raman image produced with this mode is determined by a combination of the laser focus area and the spacing between the acquisition points in the scanning grid.
      • point-by-point mapping mode
        -- def.: A mapping mode in which the laser beam is specifed to be focused to a spot.
      • line focus mapping mode
        -- def.: A mapping mode in which the laser beam is specifed to be focused to a line.

With these we might then be in the position to define the subclasses of an also new class Raman mapping?

• OBI:planned process
  • OBI:assay
    • Raman mapping
      -- def.: An assay implementing a mapping mode, in which the signal intensity or signal energy (band position) of a particular Raman vibrational mode or the intensity ratio of two Raman vibrational modes are mapped by undertaking Raman spectroscopy (2.5.17) while pointwise scanning the sample surface and subsequently evaluating each pixel of the image.
      -- source: ISO 18115-3 2.5.14

sources used

• https://doi.org/10.5772/66097
• https://doi.org/10.1016/B978-0-12-849883-5.00006-1 (via https://www.sciencedirect.com/topics/chemistry/raman-imaging)
• https://www.horiba.com/int/scientific/technologies/raman-imaging-and-spectroscopy/recording-spectral-images-and-profiles/
• https://www.horiba.com/int/scientific/technologies/raman-imaging-and-spectroscopy/raman-analysis/
• https://www.renishaw.com/en/raman-images-explained--25810

[Zack-83]

Hallo Philip,

we can live with this classification, with minor changes:

METHOD SPECIFICATION

• IAO:plan specification
  • Raman mapping specification
    -- synonym: Raman imaging specification | Raman acquisition specification
    -- def.: A plan specification that defines the spatial coverage of a Raman spectroscopy experiment, by determining whether to produce a Raman image of the region of interest (ROI) from a single acquisitions or instead from multiple mapped scans.
    • Raman single-point mapping specification
      -- def: A Raman mapping specification in which the region of interest (ROI) is covered at once, by focusing the laser beam to cover the whole ROI.
      -- comment: The spatial resolution of a Raman image produced with this mode is determined by the magnification of the optics in the system and the size of the elements in the detector.
    • Raman point-by-point mapping specification
      -- def.: A Raman mapping specification in which the region of interest (ROI) is scanned sequentially, by displacing a focused steady laser beam narrower than the ROI at different locations on the sample within an equally spaced grid spanning the ROI.
      -- comment: The spatial resolution of a Raman image produced with this mode is determined by a combination of the laser focus area and the spacing between the acquisition points in the scanning grid.
    • Raman line-focus mapping specification
      -- def.: A mapping specification in which the laser beam is specifed to be focused to a line.

PROCEDURE

• OBI:planned process
  • OBI:assay
    • Raman mapping
      -- synonym: Raman imaging | Raman spectral mapping | Raman spectral imaging
      -- def.: An assay implementing a Raman mapping specification, in which the signal intensity or signal energy (band position) of a particular Raman vibrational mode or the intensity ratio of two Raman vibrational modes are mapped by undertaking Raman spectroscopy while pointwise scanning the sample surface and subsequently evaluating each pixel of the image.
      -- source: ISO 18115-3 3.5.14

RESULT

• ...:???
  • ...:???
    • Raman map
      -- def.: an image produced via a Raman mapping.
      * Raman 0D map
      * Raman horizontal 1D map
      * Raman vertical 1D map
      * Raman horizontal 2D map
      * Raman vertical 2D map
      * Raman 3D map

[StroemPhi]

The assay type Raman mapping was already defined in CHMO, where it is called 'Raman microscopy' and 'Raman mapping' as well as 'Raman imaging' are provided as synonyms. We thus imported this class from CHMO (see: #127)