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PomBase curation
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GO slim unexplained annotation drops between stage and dev #765

Closed ValWood closed 8 years ago

ValWood commented 8 years ago

membrane organization 17 DNA replication 9

ValWood commented 8 years ago

DNA replication non issue, its transposons (although that does imply a change in parenage at GO?)

ValWood commented 8 years ago

OK the membrane drop is largely due to a drop we see because SNAP receptor activy, which has F-P link to membrane organization (via membrane fusion).

We wouldn't have picked this up, but it was included inadvertently last month when Mark included the MF in the GO slim. The point here was that Mark didn't need to do this, and we only wanted to show process slim headings on the process terms, and we _should_already of had all the process annotations.

So, SNAP receptor activity should have an F-P annotation to GO:0061025 membrane fusion

This is weird, because we do pick up quite a lot of F-P annotations Possible causes

i) GO aren't updating ii) GOA aren't updating (I don't think it can be us, as I think we get the F-P links from GOA?...double check that)

relation added 2015-01-12 Added RELATION part of GO:0061025 (membrane fusion)

Kim, first could you check the GOA files. I'll upload a gene list in a sec...

ValWood commented 8 years ago

SPBC31E1.04 SPAC4G8.10 SPBC8D2.14c SPAC823.05c SPBC2A9.08c SPCC895.04c SPBC3B9.10 SPBC36B7.07 SPAP14E8.03 SPAC23A1.15c SPBC13G1.11 SPAC6F12.03c SPAC6G9.11 SPAC31A2.13c SPAC23C4.13 SPAC17G6.07c

ValWood commented 8 years ago

should have GO:0061025 membrane fusion from GOC in GOA file

ValWood commented 8 years ago

same story phospholipid-translocating ATPase activity FP part_of phospholipid translocation

mah11 commented 8 years ago

I'm 99% certain that the GO:0061025 annotation problem is just a synchronization issue.

GOA has nothing to do with our MF-BP annotations. We get F-P inferences from the gene_association.pombase.inf.gaf file, which is generated by the owltools processes run for the Jenkins checks. At present Kim must be using the .inf.gaf from the v55 release, which doesn't have the inferred GO:0061025 annotations (see http://build.berkeleybop.org/view/GAF/job/gaf-check-pombase/95/). But when I ran the owltools checks locally for v56, the annotations got inferred, so we should pick them up in due course.

If the GAF we commit for v56 doesn't yield all the annotations we expect in its .inf.gaf we can squawk to GO about it.

ValWood commented 8 years ago

Hmm, then something smells funny to me because these links have been in GO for ages.... anyway we'll watch this space...

mah11 commented 8 years ago

Yup, whatever's going awry is happening at the GO inference step. If the problem doesn't magically sort itself when I commit the v56 GAF I'll holler at GO and post a linky here.

mah11 commented 8 years ago

opened https://github.com/geneontology/go-site/issues/2226

(I also just realized that the inferred-GAF anomaly has plagued the last few Jenkins runs, at least as far back as v54. So that problem wouldn't explain slim count changes from v55 to v56.)

ValWood commented 8 years ago

something isn't updating here because SPBC31E1.04 still has no annotation to membrane fusion even though it is encoded in the F-P links...

mah11 commented 8 years ago

It's the same problem as before -- GO hasn't acted on the ticket I opened two months ago (linked above).

ValWood commented 8 years ago

We can close this. Problem is at GO