Manager Call 2020-09-16
- Present:
- Regrets:
Agenda
Projects updates
Anyone has blocking issues/delays/changes in project scope they need to report to managers /PIs?
GAF 2.2 and GPAD/GPI 2.0 (Kimberly)
- When do we want to make an announcement to the user community?
- This seems dependent upon a firm date for switchover - do we have that?
- We should also supply a test file for developers and include its location in the announcement.
- MGI and WB are nearly ready with their files; based on 2020-09-15 annotation call, other groups are coming along
- Propose a meeting between David, Kimberly, Helen, Penelope, and Alex to discuss UniProt files wrt timing of new file release and relations used
- Expect that we will need to continue to provide support (questions, clarifications) to groups as we get closer to the switchover
Ongoing projects updates
- Noctua Imports (#3a)
- MGI/Wormbase imports
- Dustin has a new import on his USC server where David and Kimberly can check models for a select number (15-20) of genes, but code is still using GPAD 1.2 for import. Upshot: this will allow us to check the current state of the import rules for any errors, but does not reflect what the final import will include, e.g. annotation metadata
- GPAD/GPI 2.0
- Minerva and GPAD output
- We need to schedule a virtual working meeting to focus on the GO-CAM GPAD output. Proposal: David and Kimberly create an agenda so we can schedule a meeting knowing what specific work needs to get done, and then find a good time for everyone. This meeting will required Ben, Jim, and Seth. Also Eric? Dustin?
- MGI/Wormbase imports
- Legacy data (#6)
Pascale, Laurent-Philippe
- 1. gp2protein, gp2RNA files, gpi files: Any preferences for keeping/dropping them ?
- 2. File names: what about users citing old filenames ? see https://github.com/geneontology/archive-reconstruction/issues/1#issuecomment-680121448
- 3. Folder structure: can we avoid repetition in folder names ? see https://github.com/geneontology/archive-reconstruction/issues/1#issuecomment-680122454 . How do we plan for future changes ? For instance if annotation files are created for species rather than groups (this would also be a breaking change for Zenodo).
- 4. File browser: use the AWS S3 of the archive (https://geneontology-tmp.s3.amazonaws.com/index.html) for both current & release.geneontology.org ?
- 5. Do we store this archive only on release.geneontology.org or do we store it also on Zenodo *now* ? Pros: Zenodo is here for "always" and free, AWS S3 could be turned off (eg if cost not paid); Cons: everything in Zenodo would have a DOI and it could easily discourage any changes to the archive folder hierarchy / file names (situation we are in)
- Noctua (#3e)
- ui implementations
- bug fixes
- ART
- ui implementations
https://github.com/geneontology/noctua-annotation-review/issues/21
- testing and release framework
- Minerva support for noctua
- Pipeline (ongoing) (#4a)
- Pathways2GO paper (#1bi)