Difference between revisions of "AmiGO 1 8"

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= Status =
= Status =
Currently [http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi beta]. RC1 is SVN r3103.
Currently in production.
= New features =
= New features =

Revision as of 14:00, 20 January 2011


Currently in production.

New features

  • Centralized internal testing (kappa)
  • GOOSE integrated into framework (GOOSE)
  • Rapid searching (live search)
  • New term details with improved graph view (term details for GO:0022008)
  • Speed--new caching sub-system for several components (see above for example)

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
    • Use caching for gp counts? [bumped--necessary? will check with auto tester later]
    • Default gp count values
    • Fix td downloads
  • Re-expose the buckets in slimmer [bumped--using new report on accordion]
  • 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 [will likely juggle frontend servers while producing indexes]
  • 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

  • Switch TE caching over from page render caching to data caching (currently evaluating sqlite3) [likely bumped in favor of new tools]
  • Term request client for SF (AKA ART) (XP term request)
    • Could this be better done in wiki?
  • Coannotation (possible coannotation interface)
  • Advanced graph visualizations [5] [6]
    • Early plugin framework done
    • Heatmap and random plugin examples
  • Workspaces, generalization of sessions (concept)
  • Addition of ubiquitous completion in boxes

Plans and TBD

  • Migrate peripheral pages to new framework (ongoing)
  • Migrate core pages over to the new framework (ongoing)
  • Relations for TE
  • Slimmer rebuild
  • Lucene
    • Replace traditional search with lucene-backed
    • Everything to consume Solr service
  • Trying Galaxy
    • In and out from AmiGO
    • Sessions via local Galaxy install
  • 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).
  • RSS update on terms and gps (could be tied to GONUTs for timeliness?)