Taxon constraint: GO:0016055 Wnt signaling pathway

[ValWood]

Please provide as much information as you can:

GO:0016055 Wnt signaling pathway

• Request to add a taxon constraint:

• • **never in taxon: **
    fungi?

[pgaudet]

There is already 'Only in Taxon | 33208 | Metazoa'

are you getting annotations? This sound already exclude fungi.

[ValWood]

Yep, see:
https://www.pombase.org/results/from/id/ed3c0b9b-6040-4dca-afaf-df4a763dc378

[pgaudet]

@dustine32 @kltm

I thought annotations that violate taxon constraints were filtered - this one is reported in the pombase error report:
ERROR - Violates GO Rule: GORULE:0000013: Taxon-appropriate annotation check -- PomBase SPBC1347.06c cki1 involved_in GO:0016055 PMID:21873635 IBA PANTHER:PTN000226268|UniProtKB:P49674 P Casein kinase I homolog 1 UniProtKB:P40233|PTN000226265 protein taxon:284812 20170228 GO_Central

but still shows up in AmiGO, and is exported in our files:

http://amigo.geneontology.org/amigo/gene_product/PomBase:SPBC1347.06c

Can you please check what is not working?

Thanks, Pascale

[kltm]

@pgaudet Just to get a feel, does it look like taxon constraints are generally not working, or are you running into a handful of cases that are getting through? Also, we can check to see if this is a new thing or if it has been slipping by us.

[kltm]

Noting that this seems to be coming from paint_pombase.

[kltm]

@dustine32 Just checking, are the paint files processed the same way as the others in the taxon filtering stage, or are those handled "upstream"?

[dustine32]

@kltm PAINT is handled a little differently as a "mixin" but the idea is that GO rule 13 is supposed to filter out these TC violations. So, if it does end up being more than a handful, something is wrong. I'm still debugging this.

[dustine32]

OK, after a lot of time spent staring at my debugger, I figured out that the "temporary post-filter" step commands just needed to add an option (-l all) to turn on ALL of the GO rules again. This option became required recently due to changes made for biolink/ontobio#544.

Confusingly, the invalid PomBase SPBC1347.06c cki1 involved_in GO:0016055 line was reported invalid as @pgaudet pointed out, making it look like the TC check rule (GO rule 13) was running. However, this rule ran only on the source pombase.gaf in the mega-step (filtering the IBA out), but not the paint_pombase.gaf in the later post-filter (adding the IBA back).

The little test in PR geneontology/go-site#1709 (comment) shows that adding this option will correctly filter out that taxon-invalid IBA line for PomBase.

[kltm]

@pgaudet This was merged into master and should be available for testing.

[pgaudet]

I still find the offending ID GO:0016055 in
http://snapshot.geneontology.org/annotations/pombase.gaf.gz
(release date: date | "2021-06-22")

Maybe this is a lag because snapshot has not ran since the merge was done?

[pgaudet]

This annotation is now gone :)