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PomBase curation
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wtf poison and antidote MF, and products #2684

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

We can give these different molecular function terms and /or products?

Would the driver poisons fit GO:0090729 toxin activity Molecular Function

Definition (GO:0090729 GONUTS page) Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom. Secondary IDs?

Then we could have "toxin inhibitor activity" too ?

ValWood commented 4 years ago

CC @lilindu

ValWood commented 4 years ago

From https://github.com/pombase/curation/issues/2264

@ValWood

Products currently look like this: https://www.pombase.org/term_genes/PBO:0002829 If we keep as wtf element and only update to

wtf meiotic driver or wtf meiotic drive-related element once tested.

I don't think all would be correctly labelled though?

The pseudogenes are also inconsistently labelled (although I I fixed that yesterday)

@mah11 Re product descriptions - I agree, we shouldn't call them all meiotic drivers because some have been tested and shown not to do meiotic drive. Also, some only do the suppression part, i.e. make antidote but not poison ...

ValWood commented 4 years ago

So we need a definitive list of which of the existing structures are poison, and which are suppressors (for GO and products)

mah11 commented 4 years ago

Maria's more recent paper has a nice summary of wtf classes and which ones have been tested (fig 1 & fig S1)

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008350

PMID:32032353

mah11 commented 4 years ago

product description updates done as best I can tell from PMID:32032353 (I haven't changed the class 3 ones from "wtf element")

I'm not convinced enough is known about molecular mechanisms to support GO MF annotations for either the poisons or the antidotes, so perhaps it would be better to open a new ticket when more details emerge.