Manager Call 2019-06-26

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Agenda

  • Agenda: Suzi
  • Minutes: Seth

Next release of Noctua

Noctua fixes and improvements desperately awaited. What is plan for next release?

  • ACTION ITEM: schedule Noctua release of production version

Next GOC meeting milestones

We still need to finalize deliverables and resources. Tasks from June 5 call: For each task, the product owner and technical lead should work together to determine the amount of time needed.

BioGrid Collaboration?

  • Rose from BioGrid has expressed interest in collaborating with GO on GO-CAMs
  • Would we like to pursue this? Probably need more information on details of their data.
  • What is the priority level?

Follow up on last week's action items

  • ACTION ITEM: follow up with SGN to see what their plan is. Right now Dustin was in contact; need to check the status.
  • Discussed the different yaml files: datasets, groups.yaml, group contacts.yaml.
  • ACTION ITEM: Improve documentation for the content of these files
  • ACTION ITEM: Look into changing the format of some files to see if they can be more useful
  • ACTION ITEM: Set up a procedure to contact 'non-core' groups ~yearly to see if they are still active (ie groups that don't attend consortium meeting or annotation calls)


  • How does Noctua development fit in these priorities?

Discussion points from previous calls

Following up on SGN/Tomato and consequences

https://github.com/geneontology/go-site/issues/1091

  • What should be the "default" state in cases like this? Filter goa, lose experimental, or have double namespaces?

How much do we want to work to "centralize" and take over this functionality now? Should this pause the next release?

  • I think for now we will accept duplicate namespaces, correct?

GO annotation in Apollo (5 mins)

Kimberly

  • EuPathDB is interested in using Apollo for functional annotation
  • We've had two ~hour-long meetings to discuss with Nathan Dunn and interested groups: Ecoli (TAMU), EuPathDB, VectorBase, WormBase-Parasite
  • Nathan is incorporating a basic GO annotation widget into Apollo with guidance from GO (Chris, Kimberly, Seth)
  • Groups using Apollo will export annotations, map to stable identifiers, and submit to GO

GO-CAM Calls

  • Currently, we have calls on the third and fourth Tuesdays of each month.
  • Curators want to discuss modeling questions (and these discussions are generally very interesting), but many issues remain unresolved at the end of the calls
  • Is there a better way to do this, e.g. a smaller working group that examines specific annotation issues and comes up with guidelines to present to everyone?

Pipeline

  • 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?

Following up on Authoritative groups procedure

Managers: do we need to change the policy ? For example SynGO annotated mouse and rat; MGI submits the SynGO annotations but not RGD (and anyway GOC would prefer to do the integration itself).

  • Documentation is here Authoritative_Database_Groups (date unknown; moved from the old GO website)
    Discussion
    • Judy: we should contact RGD (Pascale: and all other impacted resources) and ask them whether they would be willing to have the SynGO data loaded directly
    • Paul: Paul S mentioned that he (wormbase) would be OK to just be able to review the data (in Noctua); the data flow doesn't need to go through wormbase
    • Proposed process:
      • SynGO data would be loaded directly into the GO database
      • SynGO data would be filtered out from the MOD/contributors files (like PAINT)
      • Authoritative databases would keep control of the annotations; they could review/give feedback (?)/edit annotations
    • Actions
      • Check whether doable (Seth?)
      • MGI and other groups stop loading SynGO annotations directly - would load by the GO pipeline
      • Paul T to contact SynGO and all impacted groups to explain the proposed process

Fate of "unmanaged" external2go files

https://github.com/geneontology/go-ontology/issues/16989

  • 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

Minutes

Present: Judy, Seth, Huaiyu, Kimberly, Suzi, Laurent, David, Pascale, Chris,

---

Noctua release item:

Judy: Why so little progress, releases?

Seth: Six month release cycle?

Kimberly: Working on ART and new form of form. Have more time for working with dev.

Judy: Release notes and roadmap for next release would be useful for communication.

Huaiyu: USC happy to help out with communication with dev.

(Catch Chris up)

Chris: Clarifying release process; wasn’t it rolling?

Kimberly: More six month cycle now, but need to spend more time with dev.

Huaiyu: Start participating on Tuesday @10am call.

Kimberly: Will look at tickets and TODO

---

Meeting milestones:

(Back to the spreadsheets, description by Pascale)

Seth: Six month projects are more minimal--MVP and what comes up.

Pascale: No more overload.

Seth: The spreadsheet document is what was, not what is, so no worries about the time. Only to decide on the projects and tickets.

Chris: So what does this mean for negative surplus?

(Accuracy vs. bellyfeel in spreadsheets - more spreadsheet poking - column X.)

---

BioGrid:

Kimberly: Data import from them to GO-CAM. Kimberly will follow-up to get more detailed info.

(Discussion of data, curation, and workflow - what are expectations.)

Chris: Maybe there are separate discussion here. Is the discussion direct curation of not?

(TODO: Kimberly: Need more info, will go back to Rose)

---

Tomato:

(TODO: Update/close 1091; SGN out, GOA in, make new ticket.)

(TODO: Seth will follow up with Dustin about the two choices forward and to make sure that this is properly communicated to SGN)

---

More info into groups.yaml?

(Pascale catching people up on state of play; will work with Suzi to see what is needed, then talk to Chris/Seth about where it would best go.)

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Annotation in Apollo:

Kimberly: Call with vectorbase eupathdb wormpath; interest in Apollo. Nathan Dunn talk with reps. Nathan got reqs and started doing work.

--- FINAL

Suzi: Propose that GO-CAM and last two items are rolled over into next agenda.