#341 inviable children and cell cycle phenotypes

[Valerie Wood]

I am annotating a phenotype which is
invivable, arrested with elongated phenotype.
I thought I should be able to get to a term for "elongated, inviable" by progressing down from "inviable"

Perhaps we need a grouping term under invaible for
"inviable vegetative cells" for cells which undergo some vegetative growth and or division under which to group the
mitotic catastrophe, cut, small inviable vegetative"

Then i think we need a child
"elongated inviable vegetative cells"
which is also a child of
elongated vegetative cells

(because I am trying to represent a single phenotype)
mitotic catastrophe belongs under here I think (that must be an inviable phenotype?)

we also need the elongated multinucleate and elongated multiseptate duplicated under the inviable node
(so essentially these terms need a viable/inviable node)

Also add synonyms "essential..." to inviable terms.

Note to self dpb3 curs/08dc04f357b0310b

[Valerie Wood]

In the same paper, the WT dpb3 knockdown
has elongated vegetative cells which arrest with less than 2C DNA content

so this could be
"mitotic cell cycle arrest in S-phase"
but I want to capture that they are elongated
so could we have
"mitotic cell cycle arrest in S-phase with elongated cells"
Child of elongated vegetative cells
?

[Valerie Wood]

This is an inviable phenotype so should be:

"mitotic cell cycle arrest in S-phase with elongated inviable cells"

For def
Cells which arrest with less than 2C DNA content and elongated cells, and is usually accompanied by a marginal increase in cell number (may be useful for parent too?)

[Midori Harris]

new terms
inviable vegetative cells FYPO:0001489
elongated inviable vegetative cells FYPO:0001490
viable vegetative cells FYPO:0001491
elongated viable vegetative cells FYPO:0001492
elongated multinucleate inviable vegetative cells FYPO:0001493
elongated multiseptate inviable vegetative cells FYPO:0001494
elongated multinucleate viable vegetative cells FYPO:0001495
elongated multiseptate viable vegetative cells FYPO:0001496
elongated inviable vegetative cells with mitotic cell cycle arrest in S phase FYPO:0001497

For FYPO:0001497, I've put the bit about cell number in a comment rather than in the def, because the phenotype is defined as cell-level.

I'm not a big fan of the "essential" related synonyms, because essential isn't a phenotype, but I've added them to help searching.

[Valerie Wood]

...just used this one. I think "cut" should go under "inviable vegetative cells" rather than just inviable?

val

[Midori Harris]

must investigate - the reasoner does that for me when I run Oort on my machine but not on the server

[Midori Harris]

update: Oort output OK; have pinged Kim about what's in the tool

[Midori Harris]

curation tool now uses reasoned fypo-simple.obo