Difference between revisions of "AmiGO 1 8"

From GO Wiki
Jump to: navigation, search
(8 intermediate revisions by 2 users not shown)
Line 1: Line 1:
= Status =
= Status =
Currently in production.
Currently in [http://amigo1.geneontology.org production] (as of 20013-10-17).
See [[AmiGO 2]] for the future beta.
= New features =
= New features =
Line 22: Line 26:
= Known issues =
= Known issues =
* Slimmer bug [https://sourceforge.net/tracker/index.php?func=detail&aid=2996853&group_id=36855&atid=908269]
Please see the [https://sourceforge.net/tracker/?group_id=36855&atid=908269 tracker].
= Deferred (alpha) features =
* <strike>Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)</strike> [likely bumped in favor of new tools]
* Term request client for SF (AKA ART) ([http://amigo.berkeleybop.org/cgi-bin/amigo/xp_term_request XP term request])
** Could this be better done in wiki?
* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
* Advanced graph visualizations [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers_graph] [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers2_graph]
** Early plugin framework done
** Heatmap and random plugin examples
* Workspaces, generalization of sessions ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=workspace_client concept])
* Addition of ubiquitous completion in boxes
** Front page with completion ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=front_page concept])
** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/go.cgi xprods in 1.5]
** [http://berkeleybop.org/alpha/goxprod/go.cgi xprods in 1.6]
***Examples (all using experimental bp_xp_mouse_anatomy xps):
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-assoc.cgi?term=MA:0000072 heart]
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-details.cgi?term=GO:0007507&session_id=159amigo1208881634 heart development]
**** [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 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?)
[[Category:Software Progress]]

Latest revision as of 14:56, 22 May 2014


Currently in production (as of 20013-10-17).

See AmiGO 2 for the future beta.

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

Please see the tracker.