Manager Call 2018-08-15

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Management of Tickets

Proposal to use org projects https://github.com/orgs/geneontology/projects/ and abandon https://github.com/orgs/geneontology/projects/1

    • What is project 1? Can we standardize the way we use projects? It was a way to replace the old management tracker. The idea

was to reflect our aims. Can we do this in another way to reflect our aims? Perhaps they should go in the descriptions. If it is to drive the progress report why not begin writing the progress report at the beginning of the year?

    • This is probably not a good way to view priorities. They should go with the individual projects.
    • Or should all projects be created at the top level?
    • Pascale uses the board to track priorities.
    • But generally the project boards would be best if they flowed from left to right.
    • We would like something at the appropriate level for the PI calls so they are aware of things.
      • We will replace project 1 with a rolling doc for the project report. We can tag projects in the repo with the aims that they address.


Monthly release delay

  • Causes? Any thing we can do to help ?
  • Releases should be announced on the go-announcement repo. Who can be responsible for this ?
    • Would it be good to have a manual process that includes news? It would go out in the announcements repo.

GO Web Site Migration

Drupal move: new home of documentation is https://github.com/geneontology/go-docs/tree/master/documentations


Job descriptions for each manager

Pascale and Kimberly stared to create job descriptions for all managers roles:

https://drive.google.com/drive/folders/1F7e2D7T4hleIq8VaH7YW60D9wxQnRFRV

Every manager should add what they believe are their tasks. And then we discuss it here.

  • Please have a look.


Pipeline - what data should groups display?

https://github.com/geneontology/paint/issues/53#issuecomment-410834662

PAINT annotations

  1. Pascale: Right now we suggest that MODs/groups consume the PAINT annotations as part of their groups' entire file (ie, including their own annotations). Does that really make sense ? I thought that the 'full annotation file' (ie, including PAINT); was meant to external users rather than for contributing groups. Given that most MODs either curate locally, or import from UniProt, does it make sense to re-import their own data via GOC *or* to filter the entire file to only import PAINT files ? See https://github.com/geneontology/go-annotation/issues/1939#issuecomment-410616491
  2. Propagation of IBD annotation to the leaf sequence when it has an experimental annotation already. For example, geneA has an EXP annotation to a GO term G, and it is used as an evidence to propagate G to its ancestor node X. The question is whether geneA should have an IBA annotation to G. In the current paint GAF, geneA is annotated to G with IBA evidence code. The reason is that geneA should be treated the same as all the other sibling genes through this evolution model. It is not a redundant annotation because this has a different evidence code. In addition, only a fraction of EXP annotations were propagated, so an IBA on top of an EXP annotation carries a heavier weight to the annotation. However, there are disagreements to this practice, because it already has the same annotation with experimental evidence code. As a result, this becomes redundant and circular. We should discuss and reach a consensus on this.
  • Should we meet with groups one-on-one.
  • What is the use case for the use of all of the data?
  • Shouldn't we strongly encourage people to use the official version of GO.

Follow up from last week

Feedback form update (UPDATED)

https://github.com/geneontology/go-site/issues/750

Did we figure out the payment? No, still on my plate (Seth)

What's the time line for deployment? TBD, but pretty much instantaneous when done. (Seth)

New GAF Submissions

SuziA: Update on documentation

Ontology Editors' Meeting

Geneva- Week of December 10th

The meeting will focus on:

  • creating good logical definitions in both a general context and in the context of the GO-Reactome-Rhea alignment
    • Filling in missing GO-Rhea xrefs
    • moving from reactions to biochemical pathways
    • implementation of a method to keep in synch with all three resources
    • GO-CAM templates for pathways??
  • potential implementation of Design Patterns and the revival of some type of TermGenie ability
  • GH ticket work and mini-project planning
  • Attendees
    • David H
    • Kimberly
    • Karen
    • Harold
    • Pascale
    • Alan B (Rhea, for at least part)
    • Anne (Rhea, for at least part)
    • Chris
    • Peter D?
    • Ben?
    • Jim?

Pascale: needed to follow up with Paul regarding funds to hold these

Review Project Priorities for each group

(Note that this should be a recurring discussion on these calls) https://github.com/orgs/geneontology/projects/1