Errors with identifiers

[pgaudet]

Hello @dustine32

According to the error reports, there are a lot of invalid IDs in PAINT files:
http://snapshot.geneontology.org/reports/gorule-report.html, rule 27, for example:

http://snapshot.geneontology.org/reports/paint_mgi-report.html#gorule-0000027
http://snapshot.geneontology.org/reports/paint_other-report.html#gorule-0000027
Can you please have a look ?

Thanks, Pascale

[dustine32]

@pgaudet This sounds related to this geneontology/go-site#765 , which involved adjusting some metadata files to allow the TAIR:locus:##### identifiers through @tonysawfordebi's GOA validation. Could it be that gorule 27 just isn't evaluating identifiers in the same fashion?

Other than the TAIR ID, I'm not sure which ID's (if they're in the with/from field) could be failing these tests. @dougli1sqrd Would you be able to pinpoint some of the failing ID's here? Could just be the double-"MGI:" dealio? Thanks!

[dustine32]

@dougli1sqrd pointed out to me yesterday that it's the "||" double-pipes in the with/from field that are triggering the error. Will need to debug the GAF generation script to further identify source of oddity.

dictyBase DDB_G0279641 sae1 GO:0016925 PMID:21873635 IBA PANTHER:PTN000102043||TAIR:locus:2159727|WB:WBGene00000142|SGD:S000006384|PomBase:SPAC4C5.04|FB:FBgn0029512|UniProtKB:Q9UBE0 P SUMO-activating enzyme subunit 1 UniProtKB:Q54WI4|PTN000860276 protein taxon:44689 20170228 GO_Central

http://release.geneontology.org/2018-10-08/reports/paint_dictybase-report.html#gorule-0000027

[pgaudet]

Can this be high priority ? It affects many annotations.

Thanks, Pascale

[dustine32]

@pgaudet Yeah, this shouldn't be too difficult to figure out before the next monthly update in a few days.

[dustine32]

Testing the fix resulted in the missing TAIR:locus:2832477 appearing in the with/from field. No double-pipes:

$ grep DDB_G0279641 2018-10-22_fullgo_test/IBA_GAFs/gene_association.paint_dictyBase.gaf | grep GO:0016925
dictyBase	DDB_G0279641	sae1		GO:0016925	PMID:21873635	IBA	PANTHER:PTN000102043|TAIR:locus:2159727|WB:WBGene00000142|SGD:S000006384|PomBase:SPAC4C5.04|TAIR:locus:2832477|FB:FBgn0029512|UniProtKB:Q9UBE0	P	SUMO-activating enzyme subunit 1	UniProtKB:Q54WI4|PTN000860276	protein	taxon:44689	20170228	GO_Central

So this should be good for this month's update.

[pgaudet]

thanks !