Difference between revisions of "AmiGO 1 8"

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(New experimental (beta) features)
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*** Default count values
*** Default count values
*** Use caching?
*** Use caching?
* Re-expose the buckets in slimmer
* Re-expose the buckets in slimmer [may be bumped if other reporting can be found]
* Update docs to most recent version (final item)
* Update docs to most recent version (final item)

Revision as of 11:32, 8 June 2010


Currently experimental.

New features

  • Centralized internal testing (kappa)
  • GOOSE integrated into framework (GOOSE)
  • Rapid searching (live search)

Current work


  • Try and lighten up on some of the POSTs in AmiGO to make searches easier to track
  • Finish new term details page--find way to avoid confusion with old view
    • Try different icons
    • Try dynamic lines to highlight ancestors
    • Explore text-based views
    • Consensus reached, now polishing
      • Default count values
      • Use caching?
  • Re-expose the buckets in slimmer [may be bumped if other reporting can be found]
  • Update docs to most recent version (final item)


  • Work out CVS to SVN transition one way or another (this will be done by June first; give production plenty of heads-up during transition) [transitioning now; seth is testing]
  • Setup production to produce their own indexes locally (don't want to shift db generation; will probably juggle frontend servers while producing indices (so much more benchmarking probably not needed))
  • See if association search index can be added/generated in a timely manner (talk to Tanya). [Takes a while--will do more work on exp server.]


  • Slimmer bug [1]
  • Upload bug [2]
  • Download GAF bug [3]
  • Links and GO.xref_abbs fun [4] [Done.]
    • To be fixed by direct download? [Yes. Done.]
  • Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)

New experimental (beta) features

  • [New] Static version of the Lucene search for fallback (term gene product).
  • Matrix tool (nmatrix)
  • Integrate new RG views from Sven (may be deferred) (phylotree)
    • Check licensing of JS tree viewer (ntree)
  • Relation filtering (may be bumped to deferred)
    • Start with term enrichment and work out

Deferred (alpha) features

Plans and TBD

  • Migrate peripheral pages to new framework (ongoing)
  • Migrate core pages over to the new framework (ongoing)
  • Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
  • Organizing annotation results by qualifier
  • Expand the scope of community annotation (depending on user feedback).
  • Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)
  • RSS update on terms and gps (could be tied to GONUTs for timeliness?)
  • Looking at other ways to supply search results (perl clucene (apache) vs. lucene (tomcat) vs. solr (tomcat or jetty) vs. perl/xapian (apache) vs. ruby/ferret (apache))
    • Look at ways of solving "*ase" problem (if it is) (e.g. reverse indexing and merge results)