Manager Call 2019-04-3
- Agenda: Pascale
- Minutes: Laurent-Philippe
Cambridge GOC Agenda
Start to firm up the agenda for GO meeting:
- Add a session to the meeting to discuss proposed and/or upcoming projects?
- This would help us to: 1) prioritize, 2) alert people to what's coming, and 3) recruit for working groups, if needed.
- Proposals: take a look at GH projects, review them and highlight major repos; be clear on priorities and get feedbacks from the consortium
- Convert the introductory google doc to a wiki doc and present it at the meeting
- It looks like we will have several new people at the Cambridge meeting. It would be good, then, if speakers were aware of this and could provide a bit of extra background for their talks.
- Present the first version of the model copy at this GOC meeting ?
- Laurent-Philippe will prepare a small presentation to highlight what is the interest and possible applications of the model copy. It should be presented after the reactome presentation and it could be nice to demonstrate a copy of a reactome model
- There should be a small face to face meeting during the GOC to fine tune date & provenance of those copies
All sessions were reviewed and people added to each presentation.
New Discussion points
- BioLink availability: plan to durably solve those issues (last week we had timeout, this morning internal server error) ?
- Reference: https://agr-jira.atlassian.net/browse/AGR-1454
- Current strategy: server api.geneontology.org up and running for more than 2 weeks. Health checks every 30s, if fails, sends sms + email notification + auto relaunch the server after 1m30. BioLink timeouts of 4s are increased to 15s as it was causing issues and the id conversion is now handled by mygene (Deepak fix). GOLr would gain to have a docker or VM that could also auto relaunch in case of failures and scale on demand.
- We need an SOP for how to handle annotation (or other?) files that have pipeline-blocking errors that can be fixed by GO
- Is it okay to fix these errors?
- If yes, then is it okay to point to a GO version of the file in the source URL in the datasets.yaml file until the source file is fixed?
- Seth to visit MGI in July? Do we have the funds to bring Seth out so he can sit with the software engineer at MGI who handles all of our loads? If we are going to create the uber-gafs at the GOC it would be nice for him to learn the ins and outs of what we do.
- Proposal: organize a meeting about data flow with architects of each MODs to speak ? or during the GOC ?
- Should Kimberly and David plan to go to visit Jim some time this spring to focus on the GPAD outputs generated from GO-CAM models?
Discussion points - carried over from last week
March release status
There was a discrepancy in March between the data available in AmiGO (Feb 2nd) and in zenodo (2019-03-10) What happened ? Is the version in the zenodo archive OK ?
Fate of "unmanaged" external2go files
- Ontology group would like to archived them since we don't have the resources to maintain them and no one is maintaining these (e.g. mips is deprecated).
Must list which projects are not maintained anymore, and at least simplify the list. Waiting from Paul review. It seems tigr will be maintained by NCBI.
external2go svn link: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/external2go/
Also looking at "Genome Properties" for GO mappings. Chris will put some slides on this for microbial annotations, possibly another grant to have sufficient resources.
Note that there has been a discussion of why the Reactome file hasn't been updated. https://github.com/geneontology/go-site/issues/1031
New IEAs (not InterPro2GO)
We decided earlier to not accept IEAs from outside groups, as all sequences would be run through the dependable InterPro2GO after uploading- but this group/method *seems* like they have more accurate annotations and higher coverage.
Long discussion last week - What's the next step ?
- I created a github project stub for this - Kimberly
- We were going to set up a call - has it be scheduled?
- Chris was going to review current specs, particularly wrt SO/MSO
- Discuss expanding the gpi file to include other entities used in annotation, particularly the With/From field. e.g. variation IDs, RNAi experiment IDs, etc.
- This has come up in discussions with several curation groups, including MGI, WB, and Zfin
- How does the GO gpi file work fit in with Alliance data files?
- Not all GO contributors are part of the Alliance, but it would be nice to have standardized file formats for other entities.
Pascale, Chris, Paul, Seth, Kimberly, Huaiyu, Suzi, Laurent-Philippe