Manager Call 2020-09-02
- 1 Agenda
- 1.1 NAR paper update
- 1.2 GOC Meeting Baltimore
- 1.3 GO-CAM Jamboree
- 1.4 Noctua capacities and expectations
- 1.5 New group: PHI-Base
- 1.6 Regulates closure
- 1.7 Process to follow for a project
- 1.8 Ongoing projects
- 1.9 Minutes
- Agenda: Suzi
- Minutes: Huaiyu
- Present: Pascale, Kimberly, Seth, Suzi, Paul T, Judy, Chris, Huaiyu, Laurent-Philippe
- Regrets: DavidH
NAR paper update
Everyone should have sent their section(s)
15 Sep deadline for update article
GOC Meeting Baltimore
Draft agenda based on priorities: https://docs.google.com/document/d/17Jo2qdNfbF58rIYI2K1dkrEWk4-JqT-2aVAb1_vgAHI/edit?usp=drive_web&ouid=116162935390241629304
- Responses to Doodle poll from:
- dictyBase - Petra
- GOC - Pascale
- SGD - Suzi
- UCL - Ruth
- UniProt - Penelope
- WB - Kimberly
- Zfin - Sabrina
- Will contact other groups (FlyBase, MGI, RGD, etc.) specifically and try to pick a date by next week
- Right now, early November is most likely
Noctua capacities and expectations
Time ran out on last meeting- any last thoughts?
New group: PHI-Base
OK - GOA will handle it for now.
- Amigo regulates closure: The current behavior is probably not the best one - regulates closure should NOT be applied by default
Summary from Software call
- Request to include regulates closure in GO enrichment tool and results from the tests.
Process to follow for a project
The different phases, the responsibility of product owner, technical lead and architect for each phase
- requirement phase
- implementation plan
- project validation
- tickets and assignment
Next week, we'll talk about aims for the rest of 2020 for each of the projects. Everyone should let us know what the 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?
Ongoing projects updates
- Noctua Imports (#3a)
- MGI/wormbase imports
- GPAD/GPI 2.0
- Minerva/gpad output
- I think we need to schedule a 1/2 or full day working meeting to focus on the GO-CAM GPAD output. Propose that David and I create an agenda so we know who needs to be at the meeting 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)
- Users expect not to include regulates closure. GO shouldn't include it in Amigo when inferring parent terms.
- Huaiyu has done the test on the enrichment by including and excluding the closure using both internal test lists and lists from Val and Ruth. Should share the results with the managers and circulate the test lists and data.
- Will invite Val and Ruth to a meeting to discuss the results.
- Will announce at the GOC meeting.
- It is under control.
- Will include GO API in the paper.
- Will not put regulates closure decision in the manuscript for now. If we reach a consensus at the GOC meeting we can add it in the revision.
- The agenda looks good. Will revisit after the GO manuscript is submitted.
- Add regulates closure topic to the agenda.
- Doodle poll sent out for dates. Not all MODs responded. KVA will reach out. Right now it's looking at early November.
- Tentatively 4 days, with 1 day project overview, 1 day in signaling pathway and 1 day in metabolic pathway.
- The document was generated after a discussion between Seth, David and Sabrina. More people should take a look and provide input.
- The purpose is to set the right expectation for the new groups who join the Noctua curation.
- Right now, when a new curator started to do Noctua curation (eg., Christina from Swissprot), neither Seth nor Kimberly were aware of it. Need better communication and set the right expectation to the curators.
- Also have the proper documentation on GO wiki.
- This could be a topic at the GO meeting.
- Seth: The document is to help people to understand the data flow. Such as data filtering. The curator may not get their own thing.
- Kimberly suggested to create a Noctua user mailing list for announcement and Noctua specific issues.
- Kimberly will take a look at the new models and new curators and communicate with them. Seth will help on the process.
Handled by GOA. Treat it as any of the other GOA group.
Process to follow
- Following the discussion of ART. Who should be involved in each phase.
- Kimberly raised a point whether the requirement phase is only between product owner and technical lead or it is helpful to have input from other developers.
- Paul clarified that requirement is the responsibility from product owner, who is free to bring anyone. Requirements should be what the users need, not what is technically possible. Once the requirements are defined by the product owner, implementation plan will be discussed with the technical lead, who may bring in other developers. If there are issues or delays in meeting the implementation milestones, they will be resolved by negotiation between product owner and technical lead.
- Seth: In the requirement, implementation and validation cycle, it is often caught up at the validation.
- Paul: The main goal is to better use people's time, so that people are not caught up in too many meetings.
- Judy: Useful to have regular demos to a focus group.