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PomBase curation
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ure4 and ure6 #771

Closed ValWood closed 8 years ago

ValWood commented 8 years ago

in the GO terms we don't annotate SPAC3A12.09c.1 GO:0006807 nitrogen compound metabolic process PomBase SPAC29A4.13.1 GO:0006807 nitrogen compound metabolic process PomBase

implies that ure4 and ure6 have lost their current annotations to urea metabolic process. Need adding back...

Antonialock commented 8 years ago

should be able to get something from here

PMID:24177583 PMID:12471450

Antonialock commented 8 years ago

thats strange though because ure4 still has /GO="aspect=P; term=urea metabolic process; qualifier=heterologous_system; GOid=GO:0019627; evidence=IGI; db_xref=PMID:26037463; with=PomBase:SPAC3A12.09c,PomBase:SPCPB16A4.05c,PomBase:SPAC29A4.13,PomBase:SPAC1952.11c; date=20151021"

(this shows on both stage and www)

there is no direct annotation to nitrogen compound metabolic process

Antonialock commented 8 years ago

yeah, ure6 also has that IGI...it was added in october.

mah11 commented 8 years ago

The excluded-GO-terms log for the v56 release does not report any annotations directly to GO:0006807. Val must have looked at the latest logs, i.e. the more recent loads that will eventually become v57, because that's when they appear.

The reason they're cropping up now is that the Chado loader is now choking on the (correctly) comma-separated 'with' field entries in the GO:0019627 annotations. Because they can't be loaded, the less specific GO:0006807 annotations don't get filtered as they were last time. I think Kim's on it -- see https://github.com/pombase/pombase-chado/issues/483 and https://github.com/pombase/pombase-chado/issues/504.

Take-home message: carry on if you like, but you don't actually have to do any annotation to fix this. It'll all be sorted by fixes to loaders, checking scripts, etc.

Antonialock commented 8 years ago

ah ok, i'll close this then, they will come through eventually..