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
Pathways2GO manuscript
ZFIN load
Seth/Sierra
Any other ongoing project
ART1.0/Noctua3.0 plan
Items not discussed at last meeting
Next sprint
https://docs.google.com/document/d/1AIuq8xxgV6bZZHFbXW-s3ln8PdUfZGNUuZcNFX1n7eQ/edit#