changes to "cut" terms (was phenotype definition query)

[fypoadmin]

bccb6092e76df671 cut query

re: check the cut phenotype thanks. They say "improper nuclear segregation in some delta-pch1 cells, resulting in one daughter cell with two nuclei and the other with none". This is cut right? But the gene doesn't have this annotation from genome-wide data.

I don't think this is "cut"

cut means the septum has "bisected" the DNA. This phenotype often accompanies cuts, but it isn't describing cut

Actually the def doesn't day this, In a cut phenotype, a cell undergoes septation despite abnormal chromosome segregation, and gives rise to inviable daughter cells.

but I am sure it is the case....its a more specific type of chromosome segregation defect. (It isn't "cut" for example if the chromosomes segregate completely into a single compartment, it sounds a bit of a russion roulette phenotype doesn't it ???)

Original comment by: ValWood

[fypoadmin]

To say it is cut you need to see that the septum is 'cutting' the uncondensed chromosomes see http://www.sciencedirect.com/science/article/pii/S0014579399013290

Original comment by: ValWood

[fypoadmin]

It seemed that the def of cut fitted what I wanted to describe....I couldn't find another term name? What would be the cirrect term

Original comment by: Antonialock

[fypoadmin]

I don't know if you can be more specific than "mitotic chromsome segregation defects". I can't really tell from that image though what the defect is.....I can tell it doesn't look right, but I don't know if it is bisected by the septum...

Original comment by: ValWood

[fypoadmin]

• Owner: Anonymous --> Midori Harris

Original comment by: mah11

[fypoadmin]

Re:

cut means the septum has "bisected" the DNA and To say it is cut you need to see that the septum is 'cutting' the uncondensed chromosomes

That's not exactly how you (and Jacky, I think) defined it way back when I created the original cut terms. The current definition is what we came up with after some emails and chatting (some of the ancient stuff is in [fission-yeast-phenotype:#9]). Cut always entails abnormal chromosome segregation, but not all abnormal chromosome segregation is cut. The essential distinguishing feature of cut is that the cell attempts septation even though chromosome segregation goes awry -- at the time, we didn't think it mattered where the septum ended up relative to the DNA (i.e. didn't affect whether it counted as cut).

On a related note, "cut" used to have two children:

[Term] id: FYPO:0000322 name: cut, septum dividing nucleus def: "A cut phenotype in which the septum forms and physically divides the nucleus into two parts." [PomBase:mah, PomBase:vw] is_a: FYPO:0000229 ! cut

[Term] id: FYPO:0000323 name: cut, binucleate cell formation def: "A cut phenotype in which septum formation produces a cell containing two nuclei." [PomBase:mah, PomBase:vw] is_a: FYPO:0000229 ! cut

As a small part of [fission-yeast-phenotype:#191] we decided to merge FYPO:0000322 and FYPO:0000323 into the parent, because the distinction wasn't important. I "replaced" them with the current comment. What's important now is that both before and after the merge, everything stayed consistent with the criteria for cut that we used in the current FYPO:0000229 def.

If you have now changed your mind, and think only the case formerly specified in FYPO:0000322 counts as cut, I can amend the ontology -- but only if you can guarantee that you won't want to change back in a few months' time.

Original comment by: mah11

[fypoadmin]

p.s. I think I wouldn't annotate pot1 or pch1 to cut, but for me the reason is that I can't tell from the micrographs whether they actually get dodgy chromosome segregation and septation in the same cells. That, in turn, could reflect the fact that I'm still not all that experienced at interpreting micrographs of pombe ...

Original comment by: mah11

[fypoadmin]

I remember having problems pinning this one down, and I did look at these earlier requests and realised it was different. However, it doesn't fit with the other defs I have seen since. I will need to re-check with Jacky.

I now think the confusion depends whether 'cut' is used to describe the cell phenotype or the population. From how I understand it "cut" cell is bisected DNA, but the phenotype always occurs at low penetrance with other phenotypes which have chromosome segregation defects, but are not 'cut' however some people call the mixed population 'cut' We probably need to pull these different uses apart and I won't get around to this soon, probably a week or two when i plan to speak to JAcky about 51 outstanding e-mail queries. Anyway I will add this one to the list.

v

Original comment by: ValWood

[fypoadmin]

discussion at 2014-01-21 curator meeting:

• Val thought old 'cut' had to take whole population into account (though all cut terms have always been cell-level)
• Now want cut restricted to cases where septum divides nucleus
• Obsolete existing 'cut' & replace with new ID, narrower def

Original comment by: mah11

[fypoadmin]

• labels: --> term obsoletion
• summary: "cut" phenotype definition query --> obsolete "cut" (was phenotype definition query)

Original comment by: mah11

[fypoadmin]

Finally getting back to this, and I have a couple of questions:

1) Do we need a term for the general case of a cell forming a septum even though chromosome segregation has gone wrong? If so, should we also include the other case, where the septum doesn't split the nucleus, so one daughter ends up with two nuclei (which probably have unequal amounts of DNA) and the other has none?

• septation following abnormal chromosome segregation -- [i] cut (aka septation following abnormal chromosome segregation, with septum dividing nucleus) -- [i] septation following abnormal chromosome segregation, with binucleate cell formation

If we do this, it will pretty much restore the old arrangement, except that the "cut" name will be used for one of the children instead of the parent.

2) Can these terms be updated to refer the new, narrower "cut"?

• FYPO:0001048 mitotic catastrophe with cut
• FYPO:0001052 mitotic catastrophe with cut, small cell
• FYPO:0001053 mitotic catastrophe with cut, normal size cell
• FYPO:0001054 mitotic catastrophe with cut, elongated cell
• FYPO:0001055 cut following normal mitotic entry
• FYPO:0002054 cut during cellular response to hydroxyurea
• FYPO:0002295 mitotic catastrophe with cut, elongated cell during cellular response to hydroxyurea

Original comment by: mah11

[fypoadmin]

septation following abnormal chromosome segregation -- [i] cut (aka septation following abnormal chromosome segregation, with septum dividing nucleus) -- [i] septation following abnormal chromosome segregation, with binucleate cell formation

this sounds good to me. I can think of one more term septation following abnormal chromosome segregation, with fragmented DNA (in either or both compartments, one nucleus may be intact)

I'm not saying to put this term(s) in now, just wanted to say that it/they might come along in the future (I have seen cells along these lines before) so just wanted to check something like this would fit in as well.

Original comment by: Antonialock

[fypoadmin]

3rd additional term sounds fine, and it would be just as easy to add it sooner rather than later

Let's see if Val likes the option with more terms ...

Original comment by: mah11

[fypoadmin]

It also occurs to me that if we do go for the more-terms option, it would be ontologically OK to just rename the existing "cut", because it's already got the "parent" definition. But maybe Val wants existing annotations flagged for review by the obsolete-catching system?

Original comment by: mah11

[fypoadmin]

Ok I agree with this. Lets try the renaming option.

Antonia can remap the HU screen annotations down to the new appropriate term(s)

I think the mitotic catastrophe ones could be placed under the new cut (at least how I have used them)

Then we would only need to check what remains annotated to the old cut to see if they need to be migrated down or not (should not be many)

Would that work?

Original comment by: ValWood

[fypoadmin]

That sounds ok.

Antonia - which term(s) would you need for the HU screen? I can either convert the existing 'cut during HU' term to use the shiny new 'cut', or leave it connected to the soon-to-be-renamed parent. If I leave it using the parent, would you need any child terms, using 'cut' or its new siblings?

I'm also assuming that 'mitotic catastrophe with cut during HU' can use the narrower new 'cut' along with the other mitotic catastrophe terms, per Val. OK?

Original comment by: mah11

[fypoadmin]

use the spiffy new 'cut' for all descendants, and hope for the best!

Original comment by: mah11

[fypoadmin]

• labels: term obsoletion --> new ontology term, other ontology change
• summary: obsolete "cut" (was phenotype definition query) --> changes to "cut" terms (was phenotype definition query)
• status: open --> closed-fixed

Original comment by: mah11

[fypoadmin]

Done!

renamed FYPO:0000229 to match its broader-than-classical-cut definition - 'septation following abnormal chromosome segregation' added new child terms cut FYPO:0003165 (narrower def than old cut) septation following abnormal chromosome segregation, with binucleate cell formation FYPO:0003166 pointed all descendants of FYPO:0000229 to FYPO:0003165 (adjusted xps, parents, etc. as needed)

Original comment by: mah11