GO:0061246 establishment or maintenance of bipolar cell polarity regulating cell shape

[ValWood]

GO:0061246 establishment or maintenance of bipolar cell polarity regulating cell shape

This term, and regulation terms are only used by PomBase. I think they are unnecessary (I requested them years ago).

Can they merge up to GO:0061246 establishment or maintenance of bipolar cell polarity

[pgaudet]

Is there a difference between

• GO:0061245 establishment or maintenance of bipolar cell polarity and its child class: GO:0035088 establishment or maintenance of apical/basal cell polarity?

according to PMID:31213986 it's the same: "There are two type of polarity: the cell intrinsic apical–basal polarity and the tissue wide polarity known as planar cell polarity."

Looks like we can merge those as well?

[pgaudet]

Also - looks like ' GO:0035089 establishment of apical/basal cell polarity' is incorrectly under both ' GO:0061162 establishment of monopolar cell polarity' and GO:0061245 establishment or maintenance of bipolar cell polarity

Is this right?

[ValWood]

@mah11 may know.....

[ValWood]

The terms might mean the same but in fission yeast we never use apical/basal because uni-cellular organismal cells don't have a 'base'

[mah11]

I cannot comment on why GO:0035089 is under both GO:0061162 and GO:0061245, nor which parent is correct.

The difference between GO:0061245 and GO:0035088 is that a cell may be bipolar without the poles corresponding to apical and basal (this is the case for fission yeast). Whether GO needs to preserve that distinction is another thing I can't help with.

[ValWood]

GO:0061246 seems to have disappeared without notice?

At least, I get a message "Session can't be approved as a term ID is not in the database: GO:0061246 " in a session with this term. (I Can still see it in QuickGO, so tagging @kimrutherford in case it is a PomBase issue)

[kimrutherford]

It looks like the term is going missing when we process go-plus.owl with OWLTools to apply the taxon constraints. We only do that for loading GO into Canto. So it's not a general PomBase problem or a GO-wide problem. It's strange because there are no taxon constraints on GO:0061246 or its parents, that I can see. The direct parent term GO:0071963 is going missing too but the other ancestor terms get through.

Is there any way this could be a problem with the ontology or the taxon constraints is it more likely to be an OWLTools problem?

[ValWood]

I'm not sure so tagging @balhoff & @pgaudet

[pgaudet]

I dont see any changes in the editors' version of the ontology - this is a question for @balhoff

[ValWood]

Also this term: GO:0060624 JSON regulation of ascospore wall (1->3)-beta-D-glucan biosynthetic process

I see this in Canto:

[balhoff]

The owltools taxon subset command is more aggressive than normal taxon constraint reasoning. In this case there is a pretty large reasoner explanation, but it includes the relation that anatomical structures start existing during or after zygote stage, zygote stage is part of embryo stage, and then embryo stage relates to all sorts of stuff that is not in yeast.

We could either do a lot of work in Uberon to make all these relationships more taxon-specific, or provide you with a different script that only removes terms over the standard taxon constraint propagation rules.

[ValWood]

I think the definition of anatomical structure related terms needs to be fixed.

Many, many anatomical structures apply to yeast.

For example GO:0005622 intracellular anatomical structure

4778/5050 fission yeast proteins are annotated to this team. I don't think you can restrict anatomical structure to be part of an 'embryo stage' it isn't correct for many many species?

[cmungall]

it's probably best to make new high priority issues for things like this, it takes a while to scroll down and realize the high priority thing has nothing to do with the issue title,

I made a separate issue:

• 23012

[ValWood]

any news on this? I am still unable to approve curation session switch some terms. We can keep these back for a while but I don't want to gett too huge of a build up.

Please let us know what we need to do at our end...

[pgaudet]

@cmungall what needs to be done? Is this a change in Uberon?

[pgaudet]

@ValWood is this still causing problems?

[ValWood]

We have a temporary fix while @balhoff is organizing a general fix.