Switch to reference genome set for AmiGO, all APIs, and data products

[kltm]

Project link

https://github.com/orgs/geneontology/projects/117

Project description

A potential continuation of https://github.com/geneontology/project-management/issues/82.

We'd like to:

1. make all available all species in AmiGO and the API; this would require changes in the pipeline, mostly with scaling
2. adding QC (currently ontobio) and GPAD output for these products
3. do full species sorting for all data products; some adjustments to downloads and announcement

For examining scope, also see: https://github.com/geneontology/pipeline/issues/246 https://github.com/geneontology/pipeline/issues/204

PI

Chris

Project owner (PO)

Pascale

Technical lead (TL)

Seth

Other personnel (OP)

Seth, Sierra, Dustin, Patrick

Technical specs

https://docs.google.com/document/d/1CU4Zp7t-wTRlcsXlMndIBr2XNUjeBxINdv-O5XPUERQ/edit

Other comments

N/A

[kltm]

@pgaudet Added new project; we'd also likely be using myself, Dustin, and/or Sierra.

[kltm]

Before digging into what we want to do, we should decide the final scope.

[pgaudet]

Updates& discussion on 2023-03-01 Managers call:

• Current load time ~ 2 days
• Seth proposes that this becomes an active project
• may need to get a new machine
• advantage is that this would be consistent with Panther & allow species-specific downloads
• Patrick can also work on this
• Announce enough in advance so that use dont have to maintain old and new files
• However: pipeline cleanup and API projects should be wrapped up before getting this started

[kltm]

Following from @pgaudet, I'm going to put some running notes on things we'll need to tackle here are we figure out the exact scope of what we're tackling:

• [ ] load time too long; this seems to be about two days; the downloads are a quarter of this; either:
  • [ ] upstream fixes this
  • [x] we create our own cache for EBI files (would need to coordinate our tooling as well)
• [ ] new hardware may help speeds and throughput a lot (@kltm already given a green light to purchase)
  • [ ] hopefully related to docker timing out as well
• [ ] communications
  • [ ] announce enough in advance so that we don't have to maintain old and new files
• [ ] logging sizes are already an issue; reduce logging in the main tools one way or another
• [ ] docker does not seem to be able to handle the very large product as part of tempfs (check); may need to figure our non-clobbering raw filesystem for mega-step
  • [ ] this may force us back to permission leaking issues we had before using tempfs
• [ ] the stats generation has a lot hard-coded and will need to be fixed up for this
• [ ] sparta-report.json generation fails (check in on exact reasons)
• [ ] if we include species reorientation:
  • [ ] downloads pages will need to be updated
  • [ ] we'll need a shuffling script at the end for GPAD/GPI and GAF outputs
• [ ] suppress and document iea filtering (see go-site branch)
• [ ] memory increases required; need new machine (above) or less runners

[kltm]

@pgaudet Talking @cmungall , maybe to better make progress with smaller incremental steps, we could unbundle the initial task of make the "142" available as GAF 2.2s.

[cmungall]

Proposed new scope for this project:

• the end-goal is to have the GAF download page (http://current.geneontology.org/products/pages/downloads.html) have the 142 reference species, broken down by species, available as GAFs
• the non-core GAFs will not go through the same QC process pipeline as the core (MOD + goa human/cow/etc)
• the implementation will be simply to take the filtered file provided by Alex (gcrp entries for 142 species; ftp://ftp.ebi.ac.uk/pub/contrib/goa/go_reference_species.gaf.gz) and bin these into separate files, one per species
• a single static HTML file will be produced
• The UI implementation will abandon the pageanated table and be a simple table with 142 rows in one page
• The table should be sortable?
• By default the sort order should prioritize the main curated species
• the columns will be
  • species
  • count
  • link to download
  • potentially: primary source (ebigoa, mgi, ...)
• there will not be separate rna/isoform files; these will be merged in. One file per species

[kltm]

@pgaudet, More talk w/Chris, assuming we're all on the same page about this, I'd probably try and push through on this myself (spinning it out as a separate project first).

[pgaudet]

Sounds good to me.

One suggestion (if doable) would be to have 2 table, one for the MODs, and one for all others, since 142 (in fact it's now 143) species is a long list to scroll through.

Thanks, Pascale

[kltm]

@pgaudet @cmungall Re-scoping this as the "strong" version; the narrow version discussed above is now https://github.com/geneontology/project-management/issues/82

[kltm]

Moving this back to "priority", as #82 will meet some initial desirable targets and unsure if the rest is on the table immediately.