Phenotypes with targets missing in extensions

[PCarme]

I spotted a couple of phenotypes from this paper PMID:19056896 which have the extension "affecting" with no target gene specified.

Opening this ticket so I remember to look into it.

[PCarme]

This is where the problem comes from

The identifier names used in the "assayed_using" extensions are probably not recognised, right @kimrutherford ?

[ValWood]

That's weird, they don't even appear to be extensions that are valid for that term! apart from the odd IDs.
Assign to me and I'll take a look.

[kimrutherford]

The identifier names used in the "assayed_using" extensions are probably not recognised, right @kimrutherford ?

Yep, it needs to be a gene ID to be recognised.

[PCarme]

From my perspective, these annotations should be turned into "decreased histone H3-K9 acetylation at protein coding gene during vegetative growth (FYPO:0007217)" with the target gene IDs as extensions, or maybe into a new FYPO term "decreased histone H3-K9 acetylation at protein coding gene promoter during vegetative growth (FYPO:0007217)"

[ValWood]

That sounds right. Could you swithch and request term if necessary.

I have a vague recollection that at one point we decided that promoters should have the IDs with -promoter, but we never fully implemented that! Also your suggestion would be much clearer.

[PCarme]

Alright, let's do that. I'll request the new terms, and approve the session with "decreased histone H3-K9 acetylation at protein coding gene during vegetative growth (FYPO:0007217)" with the gene IDs as extensions and "promoter" as a Comment until the new terms get added.