Update "propagation phase contrast microtomography" - PaNET01210

[rduyme]

PaNET01210 is "propagation phase contrast microtomography" (no acronym)

But "propagation phase contrast synchrotron radiation microtomography" name seems to be better name, technique seems to be used only with x-rays ( with acronym "PPC-SRµCT" )

see google scholar :

• PPC-SRµCT => https://scholar.google.com/scholar?hl=fr&as_sdt=0%2C5&q=%22PPC-SR%C2%B5CT%22&btnG=
• PPC-µCT => https://scholar.google.com/scholar?hl=fr&as_sdt=0%2C5&q=%22PPC-%C2%B5CT%22&btnG=

It seems there is no link to "x-ray probe" from PaNET01210

Could we update ontology to have "propagation phase contrast synchrotron radiation microtomography" instead of "propagation phase contrast microtomography"

[spc93]

Yes we can (and should) update this term. I think the existing label is OK as it is in comon use. We could add the proposed new label as an alternate label. This would then give as labels both the commonly-used label and a better, more explicit one.

I think there is a wider question here. Taking tomography as an example, and looking at tomography techniques in PaNET that do not subclass 'x-ray probe': Which of these are, in reality, x-ray techniques (and therefore need to subclass 'x-ray probe'), and which may or may not be x-ray techniques, in which case need aditional, more specific, subclasses.

I will look at all the tomography techniques to see if we need to subclass 'x-ray probe' for any of the others.

I wasn't able to find where we put code snippets, so if anyone can remember...

[gkoum]

The use of an alt label is recommended in this case to have them both available as @spc93 suggested.

As for the wider question we could have another issue to track which tomography techniques should have "x-ray probe" as a parent class. In this case we need to be careful if these techniques have parents connected to "x-ray probe" making the classes under discussion also connected. For that we could use DL-query tab in Protege that shows all parent classes of a class.

[spc93]

definition of 'propagation phase contrast microtomography' (subclass of 'propagation phase contrast tomography')

Solution 1: Keep these terms as they are but create additional x-ray versions e.g. 'x-ray propagation phase contrast tomography' (superclass of 'x-ray tomography' etc, rather than 'tomography'), and 'x-ray propagation phase contrast microtomography' as a subclass of 'x-ray propagation phase contrast tomography'. Then need to decide which labels (and new labels) belong to which techniques.

Solution 2: As above but rather than creating additional terms, re-use these to refer explicitly to x-rays.

Solution 1 is more general and extensible, allowing these techniques to be use with future highly coherent neutron sources. However, this approach leads to a proliferation of terms.

I would suggest solution (1).

We might also state that 'x-ray probe' and 'neutron probe' are disjoint. Again, this is a pragmatic choice (which will help in finding logical inconsistencies) but would make it difficult to describe a future x-ray/neutron beamline. (Anyone planning to build one??!!).

If we decide on a general approach then I can propose specific new definitions.

[gkoum]

Solution 1 is indeed a better choice for the following reasons:

• Allows for a more future-proof approach by creating terms that are not tied specifically to X-rays. New techniques using different types of probes, such as neutrons (or other beams??), could emerge in the future and easily added.
• By keeping terms like "propagation phase contrast tomography" general and introducing subclasses for specific probes (e.g., X-ray, neutron), we're allowing the ontology to grow in a controlled and scalable manner. It is not a big ontology and it would be good to have more concepts in there highlighting their differences for example based on probe.
• Maintains a clean hierarchical structure, where you can distinguish between different types of probes and their associated techniques.

Disjoined

• Defining "X-ray probe" and "neutron probe" as disjoint is also helpful in avoiding logical inconsistencies, as it makes it clear that techniques using different probes are distinct. This makes it easier to reason about techniques using a reasoner as well as with using DL or SPARQL queries. Later if this is not true anymore the reasoner will locate the inconsistency and demand an ontology update when a technique that combines them is added. For now it is true and we can capture it in our ontology.

[spc93]

Comments on this would be helpful:

Proposed changes:

1. New term: 'x-ray propagation phase contrast tomography' subclass of: 'propagation phase contrast tomography' AND 'x-ray probe'

2. New term: 'x-ray propagation phase contrast microtomography' subclass of: 'x-ray propagation phase contrast tomography' AND 'microscopy' alt-label: 'PPC-SRμCT'

3. Modification: 'photon probe' disjoint with 'neutron probe' (previously no disjoint classes).

[paulmillar]

Just a thought: should the new term 'x-ray propagation phase contrast microtomography' should be a subclass of 'x-ray microscopy'. This would be a more specific term.