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Harmonize raman spectroscopy with obi assay pattern #129

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StroemPhi wants to merge 20 commits into main from Harmonize-Raman-Spectroscopy-with-obi-assay-pattern

docs/images/Raman_spectroscopy_Pattern.png

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Zack-83 May 17, 2024

The right panel is somehow readable for someone who understands OWL. But yet the definition looks too complex. "Raman scattering" and "Raman spectroscopy" are really too far from each other. In my opinion, we should introduce once an object property "technique implements phenomenon" and then include in it all restrictions.

The left panel does not help at all, sorry. Apparently such a graphical representation is not adapt to capture che complexity of multiple restrictions defined through unnamed nodes. So better leave it away, or replace it with something less picky but more understandable.

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StroemPhi May 17, 2024

Regarding the right panel comment:
While I agree that it looks complicated for someone not versed in OWL, this proposal follows the OBI pattern (see also: https://nfdi4chem.github.io/VibrationalSpectroscopyOntology/design_patterns/#defining-an-assay-according-to-the-obi-core-assay-pattern) and since CHMO is an OBI extentsion and VIBSO is planned as a CHMO extention, we must follow the design patterns of OBI.

But this doesn't mean I'm objecting to defining such an object property to make things easier for those kinds of assays that can be defined as methods that cause and detect a natural process (effect). As written in the notes of our last dev call importing SSN:detects won't be suitable for this. To be in line with OBO a possible parent for such a property could be RO:causally upstream of or within, which connects two causally related processes.

However, we still would want to have axioms that specify what kind of input and output such an assay has. Hence, formalizing that the evaluated material entity in such an assay is the cause of the detected natural effect seems important to me. To reduce the complexity on that part, we could define for example a "Raman spectroscopy evaluant" class as a

('material entity'
     and ('has role' some ('evaluant role' and ('realized in' some 'Raman spectroscopy'))
     and ('causal agent in process' some 'Stokes Raman scattering'))

and then just assert on Raman spectroscopy: has_specified_input some 'Raman spectroscopy evaluant'.

And we could do so similarly for the data item produced by a Raman spectroscopy, which we might want to label "Raman spectral data" and which would serve as parent for all types of data outputs of Raman spectroscopies, the unprocessed ones, like "Raman raw data", as well as the ones produced by a post-processing step, such as the plot of the spectrum.

Regarding the left panel comment:
I don't get what you mean. It is of course a reduction, but it contains as nodes and edges all asserted and inherited axioms of Raman spectroscopy. Hence it was only meant to illustrate the pattern, which imho makes it easier to see the similarities/closeness to the OBI:assay pattern.

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StroemPhi May 17, 2024 •

edited

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How about using as direct relation between Raman spectroscopy and the Raman scattering it detects RO:regulates?
It is defined as a causal relation between processes:

p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.

So we could assert the subclassOf axiom:

'scattering spectroscopy' and ('regulated by' some 'Raman scattering')

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