Projects stand up meeting 2021-03-03

Attendees

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

Projects presentation

Template:

• 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 http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/ - 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

ZFIN load

Seth/Sierra

Next sprint

https://docs.google.com/document/d/1AIuq8xxgV6bZZHFbXW-s3ln8PdUfZGNUuZcNFX1n7eQ/edit#