AmiGO 1 8

Status

In discussion--currently this is a close descendant of 1.7.

Currently experimental.

Planned Features

• TBD...

Done Features

• Centralized testing (kappa)
• GOOSE integrated into framework (GOOSE)

Current work

Future work in progress (visible in live experimental)

• Switch over to Lucene for searching
  • Addition of ubiquitous completion in boxes
• Matrix tool (nmatrix)

Planned features

• Redo of term info/tree view in all locations
  • Neighborhood-based view
• Relation filtering
  • Start with term enrichment and work out
• Revisit reference genome views and pages
  • phylogenic tree
• Migrate peripheral pages to new framework
• Migrate core pages over to the new framework
  • Front page with completion (concept)

Deferred features

• Organizing annotation results by qualifier
• Term request client for SF (AKA ART)
  • could this be better done in wiki?
• Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
  • 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)

TBD

• Coannotation (possible coannotation interface)
• advanced graph visualizations [1] [2]
  • early plugin framework done
  • heatmap and random plugin examples
• Workspaces, generalization of sessions (concept)
• 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)