Final tasks for migration to GPAD/GPI 2.0

[pgaudet]

Hi everyone,

These are the tasks needed to finalize the switch to emitting GPAD/GAF2.0. (I tentatively assigned people but not 100% about the assignments):

• [ ] @LiNiMGI to add an example GPAD with all types of examples (with extensions, with isoforms, etc) here: https://drive.google.com/drive/folders/1apwGcSv_VBcat816YM5gRDUB-FkmCebE
• [x] @sierra-moxon to produce a corresponding GPI file – this can be the ‘normal’ MGI GPI2.0, (minus any errors?), save in the same folder https://drive.google.com/drive/folders/1apwGcSv_VBcat816YM5gRDUB-FkmCebE
• [x] @sierra-moxon to check that our parsers don’t get errors for these files before publicizing
• [ ] @kltm to generate links to these files
• [ ] @suzialeksander to fix the GO website to refer to the GPAD/GPI2.0 documentation as the main file format, and more previous documentation
• [ ] @suzialeksander to announce to go-consortium and GH go-annoucement repo (+ Alliance forum? other places) under deprecated formats (https://geneontology.org/docs/deprecated-products-and-formats/)

I think we can aim for the May 2024 GO release, if this announcement can be sent in the ext week.

Thanks, Pascale

[sierra-moxon]

Hi @pgaudet - w/re to GPI, as I understand it (which may be wrong) the regular GO pipeline produces the GPI for us by default (and it is being produced in my pipeline now: http://skyhook.berkeleybop.org/full-issue-325-gopreprocess/annotations/mgi.gpi.gz). Is this correct?

[pgaudet]

This issue is GPI2.0 merges columns 1 and 2, compared with GPI1.2, see https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md

so, as far I can tell, it seems this is a different format, we cannot use the GPI that used to be produced.

Right?

Thanks, Pascale