Manager Call 2019-06-05

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  • Agenda: David
  • Minutes: Kimberly


  • The ontology shown in AmiGO is NOT the same version as that of the /release/ontology.

There is an intermediate file (go-gaf.owl) being used for AmiGO. We need to ask checks to make sure the go part of the file is the same as the one in /release/ontology. -> Is anyone available from the software group to help with that  ?

Next GOC meeting milestones

Everyone was to fill in their effort (number of days until the GO meeting) for each Priority 1 project.

Meetings (actual and proposed)

June USC Meeting

Meeting to discuss agenda scheduled for next Monday

  • Projects SOP

Kimberly and David visit Jim?

  • Remove regulates_o_part-of chains
  • Spatial relations
  • Finalize GPAD outputs from GO-CAM models
  • Streamline the ontology import process

Pathways2GO NYC at end of August?

  • Prepare manuscript



  1.  Can we delete all 'retired' pages ?
  2. Categories: @chris: is it possible to search/group pages with multiple categories? Otherwise I would like to assign single categories (and more informative) per page.

Meeting with MOD developers to go over GO pipeline?

Similar to Seth and Lori at MGI

Other business

Following up on 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?

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

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)
    • 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

GO annotation in Apollo (5 mins)


  • 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?


  • 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?

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:

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.


Present: David, Kimberly, Laurent-Philippe, Pascale, Paul, Seth, Suzi A

Regrets: Chris, Judy


  • What is the relation between the ontology file produced by the pipeline and what is shown in AmiGO?
  • LP: release should only be triggered when the GOLR instance is updated/deployed.
  • SC: for the latest release, the build environment was slightly different from Jim's local environment; the release needs to be re-built
    • the build still results in some bugs that need to be addressed; these can lead to new checks
  • PT: can we use the same files for AmiGO that users would download?
  • SC: this is what was believed to be happening, so now looking at various ways to track the files through the build process to prevent similar problems in the future

Next GOC meeting milestones

  • Taken the priority 1 tasks and assigned people
  • Does time = needed or does time = had ?
    • What was intended for time estimates?
    • time = needed
  • For each task, the product owner and technical lead should work together to determine the amount of time needed.
  • Still need some clarifications on people's time, e.g. Eric, Karen, Laurent-Philippe