Manager Call 2019-06-12

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Agenda

  • Agenda: Kimberly
  • Minutes: Pascale for Huaiyu

GO conference calls during hackathon

  • Which meetings to cancel?

Next GOC meeting milestones

Tasks from last week: For each task, the product owner and technical lead should work together to determine the amount of time needed.

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: Chris, David, Judy, Kimberly, Laurent-Philippe, Pascale, Seth, Suzi A

Regrets: Paul, Huaiyu


GO conference calls during hackathon

  • Which meetings to cancel? Ontology, Managers, GO-CAM

Next GOC meeting milestones

Tasks from last week: For each task, the product owner and technical lead should work together to determine the amount of time needed.

  • Not yet done. Chris proposes to discuss at least some of them next week (at least pipeline stuff)

Following up on SGN/Tomato and consequences

https://github.com/geneontology/go-site/issues/1091 We currently allow two namespaces (~ie 2 sources)

  • 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)