Open cboelling opened 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.
Consider obsoleting 'ictal' PATO:0001913. Consider using 'seizure'.
@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
related to https://github.com/pato-ontology/pato/issues/488 @rays22 I'm going to unassign myself from this ticket, hope that's ok
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.
@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
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?
I would need to look at the publications.
https://github.com/oborel/obo-relations/issues/633 might be of interest in this context as well.
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:
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?