cut during cellular response to HUcut during cellular response to HU

[fypoadmin]

cut during cellular response to HU

Original comment by: Antonialock

[fypoadmin]

cut during cellular response to hydroxyurea FYPO:0002054

This has made me think uncomfortable thoughts about propagating phenotype annotations ...

Cut is a child of inviable, so anything annotated to cut is counted as annotated to inviable. But will that be interpreted as meaning "never viable"? Argh.

I've added the new term anyway, because the propagation issue is there no matter whether we pre-compose or use cut + condition=in HU. Something to keep in mind, and discuss some time ...

Original comment by: mah11

[fypoadmin]

• labels: --> new ontology term
• status: open --> closed-accepted
• assigned_to: Midori Harris

Original comment by: mah11

[fypoadmin]

I think even though all of the population do not display the "cut " defect, when this defect does occur the entire population is inviable (at least that is what I understood from Jacky, although now I'm not entirely sure....I will double check this....if this is not the case, then I don't think cut should have invaible phenotype. Ergo, maybe inviable should only be the parent if the inviability is "fully penetrant"

Or you might mean, that this is only conditionally cut, so the allele can be viable in some condition and viable in others. If this is what you mean, we have discussed this before ( we discussed it in one of the curator sessions after Antonia reilised it). I think it is OK, though ...some genes will have annotations to both inviable and viable dependent on conditions and alleles..... So currently 56 genes have both inviable and viable (for different alleles/conditions) cdc2 has both, selection and some ts alleles are inviable and cdc2-3w is viable

One consistency check we could do is a check for different viability for the same allele/conditions.

Later people will be able to query more preciseley when the options to include conditions asr included. (this might not be what you meant but I though I would add it anyway...)

Original comment by: ValWood

[fypoadmin]

OK I found a few "vaibale cuts including pmt3 and cbf11, so here I think the simplest thing would be to remove "inviable " from cut...my mistake....would that solve your problem?

VAl

Original comment by: ValWood

[fypoadmin]

Thinking about this some more, when most people think about viability it is a population level phenotype, i.e for all of the deletion project, the entire population is invible, rather than individual cells. I think we need this split, and move the existing (most of) to "inviable population of cells" or "viable population of cells"

Then "cut" could still have an inviable parent, but it would be an inviable cell phenotype"...does that make sense? or am I talking nonsense?

Original comment by: ValWood

[fypoadmin]

OK, this is definitely touching on more than one thing now.

A) First I'll tackle what's going on at the level of the individual cell. For this, I'll assume that "viable" and "inviable" refer to whether a cell is alive or dead; I'll come back to the population stuff afterwards.

1)

I think even though all of the population do not display the "cut " defect, when this defect does occur the entire population is inviable (at least that is what I understood from Jacky, although now I'm not entirely sure....I will double check this....if this is not the case, then I don't think cut should have invaible phenotype. Ergo, maybe inviable should only be the parent if the inviability is "fully penetrant"

and

OK I found a few "vaibale cuts including pmt3 and cbf11, so here I think the simplest thing would be to remove "inviable " from cut...my mistake....would that solve your problem?

No. This is bringing penetrance in again.

The key question is: Does any cell that goes cut ever live to tell the tale? Or, the other way round: Is every cut cell dead?

If it's 'no' to the first / 'yes' to the second, then cut belongs under [cell-level] inviable.

What do you mean by "viable cuts"? If you have a population in which some cells are cut and other cells are alive, that's cut with incomplete penetrance. Only if you have a cell that is both cut and alive do we have to take cut out from under inviable.

2)

Or you might mean, that this is only conditionally cut, so the allele can be viable in some condition and viable in others

Yes, this is the issue. Different alleles aren't a problem at all -- different phenotypes for different alleles will all come up in search results at the level of the gene, but nobody will have any trouble figuring out what's going on if one allele

The issue is when one allele has one phenotype under one set of conditions, and a different phenotype under another set of conditions. It's not exactly a problem to annotate both, because it's an accurate reflection of what's going on; it just has more potential to confuse people because they probably won't be as quick to notice condition info and grasp its implications.

I agree that it will help to have searchable conditions. Until then, I think we just have to be aware of the potential for confusion, and ready to do plenty of explaining.

B) Now on to cell vs. cell population considerations

Thinking about this some more, when most people think about viability it is a population level phenotype, i.e for all of the deletion project, the entire population is invible, rather than individual cells.

Interesting. I wonder if other communities think similarly ..?

For microorganisms I suspect viability is often assayed by methods -- e.g. colonies on plates -- that wouldn't easily detect cases where a phenotype is incompletely penetrant but "inviable" for the cells in which it does occur.

I think we need this split, and move the existing (most of) to "inviable population of cells" or "viable population of cells"

This is a good point - a split would help us get our heads round some things. I would argue, though, that most of the viable and inviable phenotype terms should stay defined as cell-level.

Certainly the existing "viable" and "inviable" terms are defined logically as applying at the level of a cell. It'll be easy enough to tidy up the text definitions and change the names (e.g. viable --> viable cell). We can describe many of the descendants, e.g. "elongated and inviable" or "small and viable", in terms of a single cell as well.

The big exception is the "cell growth" branch. As noted in [fission-yeast-phenotype:#680], we've been muddling up growth (i.e. size increase by metabolism) of individual cells and growth of populations.

Then "cut" could still have an inviable parent, but it would be an inviable cell phenotype"...does that make sense? or am I talking nonsense?

This bit very much does make sense.

I'll open a ticket for some changes ...

Original comment by: mah11

[fypoadmin]

[fission-yeast-phenotype:#692] is now open ... let's carry on the discussion there

Original comment by: mah11