Manager Call 2017-09-06

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Joining the Call on Zoom

https://stanford.zoom.us/j/754529609

Agenda

Managers' Calls

With the personnel shuffling, we need to redo the rota for these calls. DONE (Pascale) - we can check together David might be be late or not able to make this call.

GOC meeting agenda

  • At annotation call, some people requested the workshops to be moved earlier in the meeting (Tuesday AM 3rd October?)

Documentation

Kimberly and Pascale

  • Documentation - current organization
    • wiki
    • github
    • github/readthedocs
    • googledocs
    • website

Proposal: Kimberly and Pascale would like to keep using the wiki

  • PROS: readthedoc high barrier to entry; we all know the wiki
  • CONS: Is GutHub easier to have one source of documentation for the website (external+ internal?)
  • Looks like GitHub documents can be embedded in wiki https://www.mediawiki.org/wiki/Extension:GitHub
  • POSSIBLE ALTERNATIVE?: GitHub does have a wiki. If people think this may be useful we can consider switching.
  • However the GitHub wiki seems to be less powerful


  • Organization of wiki:
    • Consortium meetings: OK how we do it now: agenda + logistics on wiki; minutes on google docs with links from the wiki
    • Annotation: Task Kimberly: Update annotation advocacy page; create a page -'Archived Annotation Advocacy and Coordination' with stale documents there
    • Ontology (to be discussed with David and Kimberly)
    • Reference genomes: Huaiyu: can we archive current pages all and put new documentation?
    • Other working groups: ask at managers call if any of these are still active
    • Community annotation: ask at managers call if this is appropriate here
    • ask at managers call whether it's OK to create a category 'Archived'
    • Progress_Reports: can those from individual WG be archived ?
    • Best practices: Most if not all should also be archived (Check with Chris and Seth)
   Annotation Policies and Guidelines: An introduction to annotation and the rules and SOPs used for annotating gene products to GO terms.
   Guide to Evidence Codes: Explanation of the codes that are used to indicate the nature of the evidence that supports a particular annotation.
   Annotation Conventions: guidelines which apply to all annotation methods and are particularly useful for manual literature-based annotation
   Annotation Standard Operating Procedures: standard operating procedures used by members of the GO Consortium during the process of annotation.
   Database groups responsible for collecting and submitting annotations for one or more species
   GO annotation reference collection
   GO annotation ("gene association") file format
   GAF Quality Control/Validation
   Annotation Quality Control checks
   GAF 2.0 annotation file format
   GAF 1.0 annotation file format (deprecated)
    • Each page would have a 'last reviewed date'
    • We would create a 'revision cycle' to periodically review all documentation


GO-CAM/Noctua development

  • Kimberly
  • What is the plan for RO development (i.e. relations and property chains) once DOS is gone?
  • Reviewing tickets in the noctua tracker this week, I am not always clear what the status is, specifically if user testing is needed.
    • Can we have/use some flavor of 'needs testing' or 'under testing' for tickets in go/noctua, go/minerva, etc.?
      • There is a 'help wanted' label in some trackers, but not all.

Status high priority tickets

  • Migration Stanford -> Berkeley
  • PAINT GAF parser (Pascale: need to check output/discuss with Huaiyu)
  • DOS transition plan:
    • Kimberly discussing with DOS
    • He will present the status of his current work on the next Ontology call (Fri Sept 8); then we can decide what needs to be done next


Minutes

Documentation decisions:

1. We'll split up the responsibilities:

  • content
  • coordination (where is it, ensuring a consistent voice, etc)

2. Order of tasks:

  • high level organization
  • use draft documentation to make more uniform/test to make sure it's informative enough
  • first task: Noctua

Action points: Define outreach role (Emily) and have a strategy call to lay out the plan

  • Have a separate call to discuss with Emily the outreach tasks: twitter, news, documentation
  • Who needs to be present: Chris, Seth, Kimberly, David, Pascale