Manager Call 2020-03-18

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Agenda

  • Agenda: Kimberly
  • Minutes: Huaiyu
  • Present: Kimberly Huaiyu, David, Chris, Pascale, Judy, Suzi, Paul T, Laurent-Phillip, Seth, Nomi
  • Regrets:

Discussion points

GO Release

Alliance is ready to make next release (1.5 weeks behind)

  • Needs new GO release to get correct GAF (affects auto descriptions)
  • GO is waiting on WB(?) ETA?
    • For WB, the fixes went in in January, but due to our release cycle, they won't make it to WB production until April
    • We could perhaps do a one-time pull from the WB development site?

Proposed solutions:

  • Ask Alliance to use old GO release (20191202 was last "good" for SGD)
  • Alliance pushes forward with known bad data
  • Alliance waits for GO release
  • Other?

Minutes:

  • SGD dropped qualifiers (contributes_to and colocalized). Suzi will talk to Mike about the issue and get it fixed.
  • To release, still use the current GO release. For the source data that has issue, trace back to the latest good release from that source.
  • Pascale: Some Ecoli annotations are lost due to its usage of old ECO codes that are filtered out during release. Will discuss with EcoCyc people.
  • Seth and Pascale will discuss details about the release.
  • The release notes will be updated accordingly.
  • WB is good...
  • PAINT lost about 7000 annotations probably related to the SGD qualifier issue. Pascale asked whether the PAINT update should ignore the qualifier. The consensus (from Paul, Huaiyu, Kimberly, David and Judy) is that the source data should be fixed. This is also a topic for the consortium as how to use qualifiers, and how to provide better guideline for the curator about using using them.

GO meeting Paris

  • What do we need to do to prepare for a virtual meeting?
  • Do we try a "node" organization ?
  • What tech to use: zoom, goto meeting ?
  • How to make those meetings more interactive / engaging ?
  • mural as a shared dashboard ? (https://mural.co)

Minutes:

  • Virtual meetings for both users meeting and the consortium meeting.
  • Due to the time differences between US and Europe, they will be half day (4 hours) meetings in the morning Pacific time.
  • Users meeting on Monday, and consortium meeting from Tuesday to Thursday.
  • Paul: Put together an agenda to see if we can fit all the items in it. This is the link to the current agenda in google doc: https://docs.google.com/document/d/1tM2kog4vvosTImB3Yym8B3r1pbDapsAMwvuDYN0K7vg/edit
  • Laurent-Phillip: For people who already registered, the registration fee will be refunded this week.
  • Will use zoom. Virtual beer hour?
  • Currently, there is no plan for local congregation.


Proposed File Format Changes

  • GPAD/GPI 2.0 specs released
    • Issue to resolve: same protein sequence maps to different transcripts and genes - one entry in gpi or multiple?
      • Propose one line for clarity (kmva)
    • Examples from current WB and UniProtKB gpi files:
Database Identifier Symbol Name Synonyms Type Taxon Parent Object ID DB xrefs Properties
WB CE01192 MSD-1 Major Sperm protein Domain containing CELE_F44D12.3 protein taxon:6239

WB:F44D12.3|WB:F44D12.5| WB:F44D12.7|WB:C35D10.11

UniProtKB:G5EEJ7
UniProtKB G5EEJ7 msd-2 MSP domain-containing protein

msd-2|msd-1|msd-3| msd-4|C35D10.11|CELE_C35D10.11| CELE_F44D12.3|CELE_F44D12.5| CELE_F44D12.7|F44D12.3| F44D12.5|F44D12.7

protein taxon:6239

WB:WBGene00009680|WB:WBGene00009682| WB:WBGene00009684|WB:WBGene00016447

db_subset=TrEMBL


  • Also, we proposed last week to make an incremental update to GAF to allow for all gp2term relations.
    • Create specs for this and share internally first for comments?
    • How soon do we need to begin preparing for downstream effects on GOC products, tools?

Minutes:

  • Released last week. Discussed at the last annotation call. A github ticket was created for feedback.
  • Ruth was concerned because her cytoscape analysis won't work after we get rid of GAF. We will assure people that we are not getting rid of GAF completely now. We will allow a transition time. Internally, we will encourage people to use/transition to GPAD/GPI.
  • Stacia raised the question about how to deal with the situation when the same protein sequence is mapped to multiple gene/transcript (see example in the table above).
  • Paul and Judy pointed out that Uniprot will demerge data and create separate entries for individual gene. We should handle it in a similar way. Will talk to UniProt about this.

MGI and WB Imports

  • Status updates
    • WB
      • Alex will work on preparing a test GPAD file with annotation history for WB - hopes to have it on the GOA ftp site some time next week
    • MGI
    • Have a periodic follow-up call to review progress?

Minutes: Did not discuss.

Pathway Genome Databases and the Alliance

See Chris' email

  • Explore bringing in other existing curated pathways in a similar way that we did for Reactome
  • Follow-up to Alliance call last week with Peter K.?

Minutes: Did not discuss.

Publications

  • Val's matrix paper is available as a draft
  • Authors have reviewed and made comments
  • Do the GO PIs (besides Chris who is last author) also need to read?

Minutes: Mentioned but was not discussed.

Proposed data flow from Alex (GOA)

  • Do we still need to discuss anything here?
  • Based on decision at PI retreat to only show in AmiGO the 142 species also included in PANTHER, i.e. fewer species but all available annotations for those species.
  • This would be a new pipeline to supplant the current UniProtGOA-all pipeline, i.e. the MODs will still be the source of their species annotations

1. All annotation sources/files are pulled to GO based on yaml files. (already implemented)

2. GOA pull them from GO based on yaml files data (partially implemented)

3. GOA perform all, so far known, sanity checks and constrains (already implemented)

4. GOA sends out reports to go-quality and group responsible for annotations (partially implemented)

5. GOA generate gpa/gpi (maybe gaf if you ask nicely) for 142 taxon for all annotations which are passed though step 3 (to be implemented)

6. GO using 142 taxon file for all their pipelines needs, no need to run their own set of checks, can be indexed directly to amigo and other tools. (to be implemented)

Minutes:

  • This was discussed at the last call and a consensus was made.
  • We are good with the plan. We need to come up with details/resources/plan.