Manager Call 2017-12-20

Agenda

Documentathon

Travel logistics. How to arrange travel for upcoming workshops.

• Before meeting, review as many existing related tickets as possible
• Best practices:
  • Have a date last reviewed on every page
• Review web pages under Documentation, FAQ
• Agenda items:
  • Annotation guidelines
    • Axes of classification for annotation guidelines
      • Term usage
      • Experiments
      • Types of gene products, e.g. transmembrane proteins
    • Evidence codes
    • Annotation relations - this is of highest priority
      • Need to be clear about the differences between relations used for GP-GO annotation, GO-CAM annotation, and the ontology
        • All relations' definitions should be reviewed, and examples provided with illustrative GO-CAM models
      • https://github.com/geneontology/go-annotation/issues/1690
      • https://github.com/geneontology/go-annotation/issues/1687
      • GAF/GPAD
      • GO-CAM
    • Annotation extensions
    • Annotation file pipelines
      • https://github.com/geneontology/go-annotation/issues/1683
      • https://github.com/geneontology/go-annotation/issues/1682
      • https://github.com/geneontology/go-annotation/issues/1674
      • Submission SOP
      • Error checks and Jenkins jobs/reports
      • Dealing with redundant annotations
  • Noctua
    • User guide
  • Readthedocs
    • Can we make better use of this?
    • Nice example of formatting: http://firefox-puppeteer.readthedocs.io/en/master/index.html
  • Using GO - extract whatever we can from the GO handbook
    • File formats available
    • Annotation basics
    • Reference proteomes vs complete proteomes
• Goals/Deliverables
  • Highest priorities:
    • Public-facing web pages
    • Noctua and GO-CAM (need to consolidate and remove links to older documentation)
      • Relations
      • User guide
      • Evidence codes
    • File pipelines
      • Annotation files
      • Ontology files
  • New documentation review by expert, new users