Clarify PATO_0001912: physiological state

cboelling commented 2 years ago

The definition of PATO_0001912 physiological state is:

A quality of a single process inhering in a bearer by virtue of the state of bearer's mechanical, physical, and biochemical processes.

The class is a subclass of PATO_0001236 process quality (A quality which inheres in an process.)

This definition is unclear to me:

What does the first occurrence of "bearer" in the above definition refer to? Is this referring to a continuant entity? If so, how does this relate to the subclassing of physiological states as process qualities?
Also, does "a [...] process inhering in a bearer" in this case is meant to refer to a process in which only the bearer, proper parts of whole, participates?
Is "the state of bearer's [...] processes" another way of refering to qualities of processes in which the bearer (whole or parts) participates? If so, doesn't this render the definition circular, or at least unintelligible?
Why referring to "single" processes? How are processes individuated?

On the whole, how does this definition relate to the intuition that a physiological state is a particular mode of being of a continuant entity, rather than a process, (presumably) in virtue of that continuant's participation in processes which bear in some way or other on the physiology?

shawntanzk commented 2 years ago

Hi @cboelling, I'm in charge of triaging tickets in PATO.

These are good questions, but I don't think I can answer them, will ping @dosumis & @cmungall who could probably give better answers.

Also I'm not 100% sure of this, but this class looks like it might be a grouping class that should not be used to annotate. If this is so, we should add a comment on this.

will also put this on the agenda for phenotype call

rays22 commented 2 years ago

Consider obsoleting 'ictal' PATO:0001913. Consider using 'seizure'.

dosumis commented 2 years ago

@cboelling - We agree that this is a confusing class. The definition is confusing. The fact that it sounds like a very general class but only has two, very specific subclasses is a bad sign. We are therefore considering obsoleting it, but first we will need to consider what to do with phenotypes where this term has been used. @ybradford will add examples.

We also reviewed the two subclasses, and are considering what to do with them. Their limited use in recording seizure phenotypes looks like it may be confusing to users. This will be addressed in #488

shawntanzk commented 2 years ago

related to https://github.com/pato-ontology/pato/issues/488 @rays22 I'm going to unassign myself from this ticket, hope that's ok

dosumis commented 2 years ago

Ping @ybradford - please can you add examples of direct usage of this term in ZFIN phenotype curation. I think this is currently a blocker on this ticket. Many thanks, David.

ybradford commented 2 years ago

@dosumis sorry for the delay - this fell off my radar. It looks like only three statements: visual perception physiological state, abnormal ZP:0012876 acetylcholine receptor activity physiological state, abnormal ZP:0009594 age-dependent general metabolic decline physiological state, abnormal ZP:0020895

dosumis commented 2 years ago

The meaning seems to be very general. I had a quick look through the phenotypes on ZFIN. I'm not sure physiological state adds anything in any of these cases:

Do you think it can just be dropped?

ybradford commented 2 years ago

I would need to look at the publications.

cboelling commented 1 year ago

https://github.com/oborel/obo-relations/issues/633 might be of interest in this context as well.

pato-ontology / pato

Clarify PATO_0001912: physiological state #483