Manager Call 2019-07-03

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Agenda

  • Agenda: Seth
  • Minutes: Pascale

Next GOC meeting milestones

Review projects - make sure all is accounted for and we can 'retire' the Google spreadsheet

Matrix Annotation reviews

Val is opening a lot of annotation review tickets based on her matrix analysis. Many of the reviews take significant time. What is the priority on this?

BioGrid Collaboration?

  • update from Kimberly
    • I'm unable to make today's call, but Rose and I have a phone conference scheduled for next Wednesday, 7/10, at 1:30pm.

Follow up on old 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. (https://github.com/geneontology/go-site/issues/1091)
  • ACTION ITEM: Document SGN /Tomato and consequences:
    • 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?
    • We will NOT accept duplicate namespaces, correct?
  • 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)
  • ACTION ITEM: More information on possible scope of BioGrid collaboration (Kimberly)

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

GO-CAM Calls (To be discussed when Paul is on)

  • 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?

Minutes

Present

Seth, Laurent-Philippe, Chris, David, Judy, Suzi, Huaiyu, Pascale

Discussion

Priorities for GOC meeting - Berkeley

  • ACTION ITEM: Need to create tickets/projects
    • Refactoring GPAD-to-RDF to use GO-CAM python library
    • Making MF a is_a BP + test effect on GO-CAM -> GPAD
    • SynGO
    • GO-CAM model and validation
    • GPAD/GPI specs: need to create new project
    • Pathways2GO

SGN issue

ACTION ITEMS: Pascale: to check whether there are tickets for these, and if these are in projects:

  • Improve documentation for the content of the go-site/metadata files
  • Look into changing the format of some go-site/metadata files to see if they can be more useful

Authoritative groups

ACTION ITEMS: Pascale, David, Suzi, Seth and Kimberly to propose how this might work

  • Chris: We need to consider that different people are creating different annotations for their non-core species; still the expert group should be responsible to oversee the quality of these annotations
  • David: The current model is that groups are responsible for the quality of their annotations. We need to check with the groups contributing annotations whether they are willing to maintain annotations; if not, the annotations need to be 'adopted' by another group, or GO-Central.
  • 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)