Issue with EcoCyc GAF

[pgaudet]

Hi @dsiegele

1. There is a problem with the EcoCyc GAF : The database name (col1) uses UniProt, instead of UniProtKB.

This means that we end up with two pages in AmiGO for the same entry:
https://amigo-staging.geneontology.io/amigo/gene_product/UniProtKB:P0A6X7 -> 2 IBA annotations
https://amigo-staging.geneontology.io/amigo/gene_product/UniProt:P0A6X7 -> 36 other annotations

Can you please edit the file and submit a new one ? And please also check the data in the withcolumn.

Only the assigned_bycolumn should have UniProt(Column 15)

Thanks, Pascale

@kltm

[pgaudet]

2. Can you also please correct COLLECTF to CollecTF?

Thanks, Pascale

[dsiegele]

Will fix these. Sorry, I misunderstood feedback in issue #1426 and changed all the instances of UniProtKB to UniProt.

"2. gorule-0000027 Each identifier in GAF is valid
~ 5000 errors
UniProtKB should be changed to UniProt"

[dsiegele]

@pgaudet @kltm

I edited the file and submitted a new one. Debby

[pgaudet]

Thanks @dsiegele

I see that the file has no header - according to the documentation (http:https://geneontology.org/docs/go-annotation-file-gaf-format-2.1/) the file needs at least the gaf version number:

!gaf-version: 2.1
(or as appropriate).

I'll let @kltm comment on whether we can parse the file without this info.

Thanks, Pascale

[kltm]

@dsiegele @pgaudet I believe that we'll be able to parse this either way. I'll start a re-run now.

Tagging @dougli1sqrd

[dsiegele]

@pgaudet @kltm OK. I'll try to figure out what I did to mess up the header and not do it again next time.