AmiGO 1 8

Status

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)

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

Known issues

• Slimmer bug [1]

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 [2] [3]
  • Early plugin framework done
  • Heatmap and random plugin examples
• Workspaces, generalization of sessions (concept)
• Addition of ubiquitous completion in boxes
  • Front page with completion (concept)
  • xprods in 1.5
  • xprods in 1.6
    • Examples (all using experimental bp_xp_mouse_anatomy xps):
      • heart
      • heart development
      • TAZ orthoset (notice heart in top right corner)

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?)