AmiGO 1 8: Difference between revisions

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== Bugs ==
== Bugs ==


* Resolve Val's slimmer bug
* Slimmer bug [https://sourceforge.net/tracker/index.php?func=detail&aid=2996853&group_id=36855&atid=908269]
* Bug [https://sourceforge.net/tracker/?func=detail&aid=2962252&group_id=36855&atid=908269]
* Upload bug [https://sourceforge.net/tracker/?func=detail&aid=2962252&group_id=36855&atid=908269]
* Bug [https://sourceforge.net/tracker/?func=detail&aid=2821450&group_id=36855&atid=908269]
* Download GAF bug [https://sourceforge.net/tracker/?func=detail&aid=2821450&group_id=36855&atid=908269]
* GO.xref_abbs fun. (seth--check on current condition)
* GO.xref_abbs fun. (seth--check on current condition)
* Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)
* Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)

Revision as of 19:49, 4 May 2010

Status

Currently experimental.

New features

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

Current work

Frontend

  • 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
  • Re-expose the buckets in slimmer
  • Update docs to most recent version (final item)

Backend

  • 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)
  • 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).

Bugs

  • Slimmer bug [1]
  • Upload bug [2]
  • Download GAF bug [3]
  • GO.xref_abbs fun. (seth--check on current condition)
  • 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

  • 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)