inviability summary

[ValWood]

http://pombase2.aska.gen.nz/gene/SPAC890.06 should be viability depends on conditions.

Can anyone help to explain?

[ValWood]

Actually it's odd because on legacy site it is also classed as vaible? http://www.pombase.org/spombe/result/SPAC890.06#fission_yeast_phenotype

@mah11 @Antonialock do you know why?

[kimrutherford]

I think it's because the inviable term for that gene ("inviable cell population" FYPO:0002059) is not a descendant of "inviable vegetative cell population" FYPO:0002061. So the code just sees the gene as viable.

See: https://github.com/pombase/curation/issues/1406#issuecomment-297328219

[ValWood]

OK that might be an annotation issue, should probably be moved down to the vegetative term... (we use vegetative terms for viability classification)

[Antonialock]

If they only say that spores are inviable I annotate to this term so please don't move it down if it is my annotation

(I annotate to inviable spore pop if they show that spores do not germinate. I annotate to inviable veg pop if they show that spores germinate but don't divide / only do a few divisions) -- Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

[Antonialock]

So unless they specifically state/show what happens then you don't know if it is spores not germinating or cells not dividing -- Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

[ValWood]

Yes OK, thats right. I have some to revisit for this purpose. Although didn't we start to sue something like "inviable spore population"?

[Antonialock]

I use inviable spore population if they show that the spores don't germinate.

Unless they say or show this you won't know if the spores didn't germinate (inviable spore pop) or germinated but didn't divide/only did a few divisions (inviable vegitative)

On Fri, 7 Jul 2017 at 11:41, Val Wood notifications@github.com wrote:

Yes OK, thats right. I have some to revisit for this purpose. Although didn't we start to sue something like "inviable spore population"?

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-- Antonia Lock, PhD PomBase Biocurator, http://www.pombase.org Department of Genetics, Evolution and Environment, The Darwin Building, University College London London WC1E 6BT, UK

[ValWood]

OK makes sense.