Projects stand up meeting 2021-03-03

From GO Wiki
Jump to navigation Jump to search


  • Present:
  • Regrets:
  • Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Judy, Paul, Chris

Projects presentation


  • Next deliverables + expected date
  • Progress
  • Issues / blockers

GAF2.2 migration status

  • Progress update:
    • UniProt: root nodes default relations -> Alex fixed last week
    • Updated gorule-0000059 to specify root nodes default relations (Kimberly will QC for WB files - should see this in rules report, when the code is updated - where/how do we know when go-rule0000059 is updated?) DONE
    • Added new gorule-0000061 to check relations in GAF2.2 files -> status:
    • David manually testing files that MGI ingest from all resources (e.g. GOC, UniProt) and subsequent release of MGI GAF2.2 (and also GPAD/GPI2.0) -> outcome and actions:
    • Double-check what GAF file format each submitting group is actually submitting (roll this into broader outreach task) -> Done on yesterday's annotation call. Have all groups responded?
  • David, Darren, Kimberly, Seth to discuss issues with GPI2.0 specs -> outcome and actions: Not sure what to tell Darren: he wanted to know where to get the gene-centric data from, what he should put in the parent column
    • Chris: PRO uses the same 'local ID', P12345, not the same 'global ID'. That 'global ID', that we reference with the prefix, is the ID we use as a reference
    • Paul: GO will not pick up a GPI file (or any file) from PRO; this comes indirectly from MGI or other groups
    • On a slightly different topic: MGI GAF has a mix of PRO and UniProt IDs in their GAF. This is not user-friendly, MGI or GO-Central should fix those
  • TO DO:
    • Annotations for external2go - make a proposal for each mapping and submit to groups that create the mappings for explicit approval (Pascale, Kimberly, David) -> TO DO
    • Kimberly, Suzi, Pascale: designing/ modifying yaml files to get full data flow from upstream soures (which files they load, how they process them, what are their default relations, ect)
    • Finalize documentation -> should be on the GO website. AI: ask Seth about deleting branch issue-2917 (will deal with GPAD/GPI2.0 specs when we get there)
    • Where else should we announce the file format change? Other forums? Send email again?
      • go-friends
      • twitter / facebook etc
      • ask Alex if he sent anything
      • announcement on - special banner
      • Specifically add Alliance email to our announcements?
      • Need to get a list of 'developers'/ GO tools developers
      • GO slack - next week
      • Reach out to people + create a new mailing list

Pathways2GO manuscript

ZFIN load


Any other ongoing project

ART1.0/Noctua3.0 plan

Items not discussed at last meeting

Next sprint