Manager Call 2020-09-09
From GO Wiki
- 1 Meta
- 2 Agenda
- 2.1 Update on SARS-CoV-2 GPI and GPAD/GAF (Chris)
- 2.2 BP annotations / regulates closure
- 2.3 NAR paper update (Laurent-Philippe)
- 2.4 GO Meeting Agenda
- 2.5 Projects updates
- Agenda: Seth
- Minutes: Pascale
- Present: Chris, Seth, Paul, Laurent-Philippe, David, Suzi, Judy, Kimberly, Huaiyu, Pascale
Update on SARS-CoV-2 GPI and GPAD/GAF (Chris)
- What should go in Col 2 ? The 'gene' is the polyprotein, so Alex is putting that in Col 2. Chris thinks the biologically relevant entity is the CHAIN.
- Sylvain Poux mentioned that in human CHAINS are getting better and better characterized.
- Suggest to do a breakout at GO meting: Alex, Patrick, Judy, Chris: decide what we need to annotate, how to extract them, and how to represent them in the GPI.
- Deliverable: GAF/GPI guidelines for CHAINS / also mention operons (for viruses but also other non-viral genes)
BP annotations / regulates closure
- From Chris: As far as I can tell at this stage we do not have a strong empirical case for excluding regulates in BP annotations.
- Paul: We do have a strong case for MF. Next week Val will attend the managers' call and give her use cases.
- Huaiyu: there is also an annotation issue - since the usage of regulates has not been consistent in the past.
- We need to think about whether it's better to introduce false positives or false negatives.
- For next grant: Use Panther and other heuristics to populate 'involved' relations, to try to have more direct annotations which should false positives in enrichment analysis
NAR paper update (Laurent-Philippe)
GO Meeting Agenda
Notes from Chris:
- can people self-assign themselves? We can also assign on the call tomorrow. Also indicate how much time you think you need.
- we have a folder for presentations but it's currently empty https://drive.google.com/drive/folders/18BUCjmSzTuy4MkVaYYQ74SNccQHlJ3HW -- we should get cracking on this!
- some of the times are a bit cryptic: "pipeline reminder". What does reminder mean here? Maybe we can flesh things out tomorrow.
goals are for each project here: https://docs.google.com/document/d/1URLkEQBewlzD-NVAjbPLWD5Gu-5xq0RysTrm1GMbuiM/edit#
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 (if not already) ready for this, but we need to assess where other groups are at
Ongoing projects updates
- Noctua Imports (#3a)
- MGI/wormbase imports
- GPAD/GPI 2.0
- Minerva/gpad output
- I think we need to schedule a virtual working meeting to focus on the GO-CAM GPAD output. Propose that David and I create an agenda so we can determine who needs to be at the meeting, what specific work needs to get done, and then find a good time for everyone. (Kimberly)
- Legacy data (#6)
- 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
- ui implementations
- testing and release framework
- Minerva support for noctua
- Pipeline (ongoing) (#4a)
- Pathways2GO paper (#1bi)