process vs. processual entity

[wdduncan]

@cmungall @matentzn @dosumis @addiehl @diatomsRcool @johnwjudkins

Ontobee shows UBERON has both process and processual entity classes. Is the processual entity intended to be the same as BFO1.1 processual entity?

Ontobee didn't provide a definition for BFO1.1 processual entity, but I seem to recall the definition being what is stated for UBERON processual entity. I'd have to do some digging to confirm/disconfirm.

However, UBERON does have a process class that uses the BFO process IRI. So, this makes me wonder:

• What is the difference between processual entity and process? So, it is unclear why they are siblings.
• Is processual entity meant to be subclass of process?
• Is process meant to be a subclass of processual entity?

I think it would be great if this was made clear.
Perhaps related to #1640

[shawntanzk]

added to agenda, will try to get an response to this

[ghost]

Discussed at the Uberon meeting... @addiehl recommends that 'processual entity' should be merged with 'process' since they are likely representing the same thing and both may be present accidentally.

[wdduncan]

@bvarner-ebi Good. I agree with him. Somewhere else (not that it matters) I think I recommended the same as @addiehl

[shawntanzk]

As this is an upper ontology change - will need sign-off from @cmungall Will bring it to his attention :) thanks!

[cmungall]

Let's solve this one here: https://github.com/OBOFoundry/COB/issues/40

[github-actions[bot]]

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[wdduncan]

This ticket has been open for a while. Any plans to address it?

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[dosumis]

Somehow missed this the first time around:

Background - we wanted this for developmental stages - which need to allow for occurrent with arbitrary temporal boundaries. In standard stage series divides development up into stages whose stage boundaries are defined by whatever morphological features are easy to score. This is, I think, different from a process like glycolysis or signal transduction.

[wdduncan]

processual entity is a BFO 1.1 concept, and in BFO 1.1 process is a child of processual entity.

Mixing BFO 1.1 and BFO 2.0 concepts in this way introduces potential ambiguities in that it is unclear how to decide whether a class should be a bfo2:process, bfo1.1:processual entity, or (perhaps) bfo1.1:process.

At present life cycle stage , is textually defined as being a kind of spatiotemporal region, which of course is not consistent to it being a child processual entity.

As far as I can tell from the definition of bfo2:process, life cycle stage can be a child of it, although linguistically it may sound a bit odd. Making such a change would address the potential ambiguities mentioned above.

[uberon]

Agreed. We need to be able to put stages in a different bucket than GO bps. I guess this grouping will have to remain in uberon until https://github.com/OBOFoundry/COB/issues/40 is resolved which has become entangled with a lot of philosophical upper ontology discussion

On Sun, Aug 27, 2023 at 6:35 AM David Osumi-Sutherland < @.***> wrote:

Somehow missed this the first time around:

Background - we wanted this for developmental stages - which need to allow for occurrent with arbitrary temporal boundaries. In standard stage series divides development up into stages whose stage boundaries are defined by whatever morphological features are easy to score. This is, I think, different from a process like glycolysis or signal transduction. [image: image] https://user-images.githubusercontent.com/112839/263531828-6c819267-3c71-4263-ba8a-2556fa97c3c2.png

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2301#issuecomment-1694670773, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGZRCC6MBW2HMOBMVG5H23XXNEIVANCNFSM5OETG2WA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[wdduncan]

We need to be able to put stages in a different bucket than GO bps.

Yes, not every process is GO bps. Not sure why or if this precludes life stage from being a child of bfo2:process.

I guess this grouping will have to remain in uberon until OBOFoundry/COB#40 is resolved which has become entangled with a lot of philosophical upper ontology discussion

If you are waiting on the COB issue to resolve, I fear you will be waiting a very, very, long time. Better to move ahead on this now.

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This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

[wdduncan]

Any update on this?