rename sensitive to thiamine starvation

pombase / fypo

Fission Yeast Phenotype Ontology

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rename sensitive to thiamine starvation #814

Closed fypoadmin closed 9 years ago

fypoadmin commented 11 years ago

rename sensitive to thiamine starvation to growth auxotrophic for thiamine?

note to self 7f4c3278d6ecc195

Original comment by: Antonialock

fypoadmin commented 11 years ago

if that fits the earlier annotations, I can change it

requested in [fission-yeast-phenotype:#561]

Original comment by: mah11

fypoadmin commented 11 years ago

hmm...not sure on second thought.

The way I used starvation was in a case where the mutant grew worse than WT. When thiamine was added to the medium growth improved (but not to level of WT).

Does auxotrophy indicate an absolute requirement?

Original comment by: Antonialock

fypoadmin commented 11 years ago

(I suppose it does? and in that case I don't want to rename the term then I want to request a thiamine auxotrophy term)

Original comment by: Antonialock

fypoadmin commented 11 years ago

Strictly speaking, auxotrophy means the cell can't synthesize something that it needs (and that a wt cell could make). In practice I think people infer auxotrophy when

they know wt cells can synthesize x, and
mutant cells don't grow in the absence of x, but
do grow in the presence of x.

I kind of suspect that "starvation" is used more for things that a wt cell would have to take up from the environment anyway ... but I haven't really tried to investigate properly, so I could be totally off ...

Original comment by: mah11

fypoadmin commented 11 years ago

I guess it would also get muddled a bit by the fact that even though cells are prototrophic for something they will still import some compounds if it is available, which may or may not trigger shutting off synthesis. And different pathways can lead to the same compound....

What would you suggest for a case where growth is improved by a substance, but it is not absolutely requrired?

Original comment by: Antonialock

fypoadmin commented 11 years ago

hmm, maybe just describe the observation with 'decreased cell population growth in absence of x'? (assuming wt doesn't show the difference with vs. without x) Then I guess auxotrophic for x could have some sort of link, maybe is_a or maybe has_output?

Original comment by: mah11

fypoadmin commented 11 years ago

hmm...ok, I'll wait with that one for a bit.

In the meantime I think you can rename that term to auxotrophic for thiamine...I'll remove the annotation that isn't auxotrophic

Original comment by: Antonialock

fypoadmin commented 11 years ago

labels: --> other ontology change
status: open --> closed-accepted
assigned_to: Midori Harris

Original comment by: mah11

fypoadmin commented 11 years ago

OK, FYPO:0001907 is now 'growth auxotrophic for thiamine'

open a new ticket if you decide you need any population growth terms

Original comment by: mah11

fypoadmin commented 11 years ago

yep. I removed the old annotation for now and am happy to leave it out. There is a difference in growth of wt with +thi compared to -thi medium. They point this out in the paper. In the paper they think the mutant exhibits "more of a difference" but tbh it doesn't look very convincing either way so I'm happy to ignore it for now..

Original comment by: Antonialock