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Seth, Amelia, Rama, Ben, Jane


~30 minutes


Went over Jane's email for as much time as we had her; got through all of the majors. Summary:


  1. Reference Genome display (major priority for 1.6)
  2. Annotation table (bulk download of annotation files by species/kingdom etc)
  3. Wiki-style user annotation (Jim Hu's API)
  4. AmiGO web services?
  5. X-product visualisation
  6. Graphical tree-view (improve on GraphViz)
  7. Flexible annotation browsing e.g. by qualifier
  8. Improve documentation


  • Display issues:
    • Minor:
      • comments
      • selecting multiple terms in tree
      • spell out evidence code acronyms
      • make NOT qualifier more prominent
      • add 'experimental' evidence group
      • reducing whitespace in results
    • Larger:
      • Highlight a list of GO terms in the tree
      • More download options
      • BLAST post-filtering results
  • Searcing
    • mis-spelled terms
    • autocomplete
    • customising data displayed in results
    • search/browse within a subset (e.g. slim) only
  • DB issues
    • remove fake root


  • It would be nice to try a quick release, so we'll try and keep this one light.
  • Majors:
    • 1, 3, 7 already mostly finished
    • 2 needs input from Chris
    • 4 is a goal to works towards
    • 5 already partially done (demo from SLC), but see 6
    • The visualization system in general needs work, Seth has had on back burned for a while to get something more powerful than graphviz.
    • 8 docs are being linked out to wiki so we can change them independent of release schedule.
  • What is release schedule for current bugfix (rama)
    • Depends on WPWG tesing (seth)
    • how about make an obo-edit-like sign off sheet (amelia)
  • [AFTER MEETING] The gene_associations file is going to have 2 new columns. Is AmiGO ready?

Action Items

  • Put together a sign-off sheet for bug release (Seth)
    • Email WG detailed list of things to check for.
  • Amelia and Seth to talk about low-hanging fruit in second tier suggestions. (Seth and Amelia)
  • Follow up on Rama's offline discussion point (see above)

Previous Action Items

  • send notes along to software group
    • amigo data structs (amelia)
    • ref gen and DBIx::Class (seth)
  • check to see what times are better for the group [DONE]
  • put all new stuff in next release tracker (seth)
  • clean tracker more