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PomBase curation
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revisit pmk1 #331

Closed pombase-admin closed 9 years ago

pombase-admin commented 11 years ago

Looking at the pmk1 page I can see lots of processes which should probably be phenotypes:

GO:0051519 activation of bipolar cell growth GO:0071854 cell wall macromolecule catabolic process involved in fungal-type cell wall disassembly (is this pathway involved in this???)

GO:0071475 cellular hyperosmotic salinity response GO:0071471 cellular response to non-ionic osmotic stress (I would group these in GO as response to osmotic stress (Unless we have any reason to believe these terms are representing 2 differnt processes are different...they appear to be the same set of genes?) Has anyone else used them, if not I suggest i) GO merges them and 2) we capture the different specific stress inducers as conditions on the phenotype annotations

GO:0000910 cytokinesis IMP Toda T et al. (1996)
GO:0071852 fungal-type cell wall organization or biogenesis IMP (look old, deltes and recurate papers)

GO:0008360 regulation of cell shape IMP

a lot of the annotation is from

Zaitsevskaya-Carter T et al. (1997)

so this seems like the key one to revisit...

Original comment by: ValWood

pombase-admin commented 10 years ago

started with this term: GO:0051519 activation of bipolar cell growth I removed all 36 BPs from this paper (regulation of cell polarity or similar). Will convert to pehnotype now.

Original comment by: Antonialock

pombase-admin commented 10 years ago

GO:0071854 pmk1 not annotated to this term any longer

Original comment by: Antonialock

pombase-admin commented 10 years ago

GO:0071475 also gone

Original comment by: Antonialock

pombase-admin commented 10 years ago

curated the Toda T et al. (1996) paper

Original comment by: Antonialock

pombase-admin commented 10 years ago

I also removed the cell shape annotation.

keeping MAPK cascade involved in cell wall organization or biogenesis (and MAPK activity involved in...) because it is involved in the cell wall integrity pathway and that term fits with that pathway?

Original comment by: Antonialock

pombase-admin commented 10 years ago

Original comment by: Antonialock

pombase-admin commented 10 years ago

i agree, sounds good

Original comment by: ValWood