pombase / fypo

Fission Yeast Phenotype Ontology
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compound terms for modifications #3658

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

I don't think we should have these compound modification terms:

increased histone H4-K5, H4-K8, H4-K12 and H4-K16 acetylation at centromere outer repeat during vegetative growth

a) it isn't sustainable b) we will only get data for proximal residues (i.e the size of the mass spec fragment) c) it would be better to be able to retrieve all increased H4-K5 increased H4-K8 increased H4-K12 individually but some modifications don't have terms, so the individual modifications are not inherited d) Because the are observed together at the same time doesn't indicate a dependency

So, if you could check that the individual modification phenotypes exist for all of the compound terms, I'll decompose the annotations.

tks

mah11 commented 4 years ago

note to self: add "at otr" terms for H4K5 | H4K8 | H4K12 | H4K16 Ac.

mah11 commented 4 years ago

OK, these have gone obsolete: FYPO:0002383 FYPO:0002384 FYPO:0003219 FYPO:0003220 FYPO:0004323 FYPO:0005317 FYPO:0005337

and these are new: increased histone H4-K5 acetylation at centromere outer repeat during vegetative growth FYPO:0007308 increased histone H4-K8 acetylation at centromere outer repeat during vegetative growth FYPO:0007309 increased histone H4-K12 acetylation at centromere outer repeat during vegetative growth FYPO:0007310 increased histone H4-K16 acetylation at centromere outer repeat during vegetative growth FYPO:0007311 increased histone H4-K5 acetylation at centromere central core during vegetative growth FYPO:0007312 increased histone H4-K8 acetylation at centromere central core during vegetative growth FYPO:0007313 increased histone H4-K12 acetylation at centromere central core during vegetative growth FYPO:0007314 increased histone H4-K8 acetylation at subtelomeric heterochromatin during vegetative growth FYPO:0007315

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