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Annotation missing from AmiGO - and not in the reports #1105
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Most basically:
So, I would hazard a couple of guesses. First, I have a hard time believing that col 2 there is legitimate in any way. Second (and the "real" reason here), this is in the goa_uniprot_all file, which we would filter as it should be in goa_human--so wrong file for taxon:9606. By design, we should not see that annotation. |
Hi,
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@kltm yes, you are right it's invalid identifier for col 2 in GAF, but it is valid col 2 for GPAD. The GOA is GPAD centric and every time we unloading GAF we need to convert it appropriately. Thanks for noticing this bug is fixed now and next release the annotations should be corrected in both human specific and goa_uniprot_all gaf files. GAF must die! |
Just to follow up on previous comment wrt other evidence codes, I've now added TAS/NAS/IC/RCA evidenced annotations to the three relevant spreadsheets. |
Great ! Thanks for the quick response. @alexsign you didn't reply about the annotation being in the wrong file; I suppose you also took care of that ? Thanks, Pascale |
@pgaudet no, there was no annotations in the wrong file. The annotations was missing from goa_human_isoform.gaf and had incorrect col 2 in goa_uniprot_all.gaf. The GOA release files on the 3rd of July will have the corrected data. Please let me know if you need them earlier. |
OK, thanks - all good, I don't think we need the data earlier, unless this bug affects many annotations ? Thanks, Pascale |
@pgaudet A release can always be done after the 3rd.
…On 6/14/19 9:40 AM, pgaudet wrote:
OK, thanks - all good, I don't think we need the data earlier, unless
this bug affects many annotations ?
(Because if you do the release on July 3rd I assume that we get this in
the August GO release, so if a lot of annotations are impacted perhaps
we'd like a new file before the next release).
Thanks, Pascale
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Hi @alexsign Thanks, Pascale |
@pgaudet I don't think I can. The annotations are in our release files (goa_human.[gaf|gpa] and goa_human_isoform.[gaf|gpa]) as well as QuickGO. I don't have an access to GOC pipeline or AmiGO. |
OK - I had understood that Col2 contained a non-valid ID. (I had assumed this should have been in Col 17 - I guess not ? ) |
@pgaudet this type of IDs are valid, we had posts about this before and it clear from file format specs. What column they are depends on the file type. goa_human_isoform.gaf it's in col 17 goa_human_isoform.gpa it's in col 2 |
OK, thanks ! |
@kltm What do we need to do to add those annotations in our set of annotations? What is not being parsed correctly ? |
@pgaudet Is this a question of adding a new GAF, or a reference to the change here https://github.com/geneontology/go-site/pull/1372/files ? |
@kltm The PR you link to is changing the file for SGN. I guess we want to make use we include goa_human_isoform.gaf. The seem to be in out products (see http://current.geneontology.org/products/pages/downloads.html) but are not in AmiGO. Thanks, Pascale |
@pgaudet We don't include any of the goa_*_isoform files; my recollection was that this was done on purpose. |
@vanaukenk Should we bring that up on an annotation call ? Thanks, Pascale |
@pgaudet |
Hello,
Reported by @RLovering
This annotation is in QuickGO but not in AmiGO. It's not in the error reports (at least not in http://release.geneontology.org/2019-06-09/reports/goa_human-report.html)
UniProtKB P05067 APP GO:0070206 PMID:19660551 IMP P Amyloid-beta precursor protein APP,A4,AD1 protein taxon:9606 20170710 ARUK-UCL occurs_in(UBERON:0000955),part_of(GO:0007568),has_input(UniProtKB:P05067:PRO_0000000093),has_output(ComplexPortal:CPX-1120),has_output(ComplexPortal:CPX-1062) UniProtKB:P05067:PRO_0000000092
Can someone check what's happening ?
Thanks, Pascale
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