Difference between revisions of "AmiGO 1 8"

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* New term details with improved graph view ([http://amigo.berkeleybop.org/cgi-bin/amigo/term_details?term=GO:0022008 term details for GO:0022008])
 
* New term details with improved graph view ([http://amigo.berkeleybop.org/cgi-bin/amigo/term_details?term=GO:0022008 term details for GO:0022008])
 
* Speed--new caching sub-system for several components (see above for example)
 
* Speed--new caching sub-system for several components (see above for example)
 
= Current work =
 
 
== Frontend==
 
 
* <strike>Try and lighten up on some of the POSTs in AmiGO to make searches easier to track</strike>
 
* <strike>Finish new term details page</strike>
 
** <strike>find way to avoid confusion with old view</strike>
 
** <strike>Try different icons</strike>
 
** <strike>Try dynamic lines to highlight ancestors</strike>
 
** <strike>Explore text-based views</strike>
 
** <strike>Consensus reached, now polishing</strike>
 
** <strike>Use caching for gp counts?</strike> [bumped--necessary? will check with auto tester later]
 
** <strike>Default gp count values</strike>
 
** <strike>Fix td downloads</strike>
 
* <strike>Re-expose the buckets in slimmer</strike> [bumped--using new report on accordion]
 
* <strike>Update docs to most recent version (final item)</strike>
 
 
== Backend ==
 
 
* <strike>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]</strike>
 
* <strike>Setup production to produce their own indexes locally</strike> [will likely juggle frontend servers while producing indexes]
 
* <strike>See if association search index can be added/generated in a timely manner (talk to Tanya).</strike> [takes a while--will do more work on exp server.]
 
 
== Bugs ==
 
 
* Slimmer bug [https://sourceforge.net/tracker/index.php?func=detail&aid=2996853&group_id=36855&atid=908269]
 
* <strike>Upload bug</strike> [https://sourceforge.net/tracker/?func=detail&aid=2962252&group_id=36855&atid=908269]
 
* <strike>Download GAF bug</strike> [https://sourceforge.net/tracker/?func=detail&aid=2821450&group_id=36855&atid=908269]
 
* <strike>Links and GO.xref_abbs fun</strike> [https://sourceforge.net/tracker/?func=detail&aid=2996856&group_id=36855&atid=908269] [Done.]
 
** <strike>To be fixed by direct download?</strike> [Yes. Done.]
 
* <strike>Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)</strike>
 
  
 
= New experimental (beta) features =
 
= New experimental (beta) features =
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* Relation filtering (may be bumped to deferred)
 
* Relation filtering (may be bumped to deferred)
 
** Start with term enrichment and work out
 
** Start with term enrichment and work out
 +
 +
= Known issues =
 +
 +
* Slimmer bug [https://sourceforge.net/tracker/index.php?func=detail&aid=2996853&group_id=36855&atid=908269]
  
 
= Deferred (alpha) features =
 
= Deferred (alpha) features =

Revision as of 14:02, 20 January 2011

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

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?)