AmiGO 1 8: Difference between revisions

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[[Category:Software]]
[[Category:AmiGO]]
= Status =
= Status =


Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental].
Currently in [http://amigo1.geneontology.org production] (as of 20013-10-17).
 
See [[AmiGO 2]] for the future beta.


= Features =
= New features =


* Centralized testing ([http://amigo.berkeleybop.org/cgi-bin/amigo/page_test?mode=kappa_results kappa])
* Centralized internal testing ([http://amigo.berkeleybop.org/cgi-bin/amigo/page_test?mode=kappa_results kappa])
* GOOSE integrated into framework ([http://amigo.berkeleybop.org/cgi-bin/amigo/goose GOOSE])
* GOOSE integrated into framework ([http://amigo.berkeleybop.org/cgi-bin/amigo/goose GOOSE])
* Live Search ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=live_search search])
* Rapid searching ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=live_search live search])
 
* New term details with improved graph view ([http://amigo.berkeleybop.org/cgi-bin/amigo/term_details?term=GO:0022008 term details for GO:0022008])
= Current work =
* Speed--new caching sub-system for several components (see above for example)
 
== 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)
= New experimental (beta) features =
* 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 ==
 
* Resolve Val's slimmer bug
* Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)
 
= Experimental features =


* [New] Static version of the Lucene search for fallback ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search_term term] [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search_gene_product gene product]).
* Matrix tool ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=nmatrix nmatrix])
* Matrix tool ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=nmatrix nmatrix])
* Integrate new RG views from Sven (likely deferred) ([http://amigo.berkeleybop.org/cgi-bin/amigo/phylotree])
* Integrate new RG views from Sven (may be deferred) ([http://amigo.berkeleybop.org/cgi-bin/amigo/phylotree phylotree])
** Check licensing of JS tree viewer ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=ntree])
** Check licensing of JS tree viewer ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=ntree ntree])
* 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
* Term request client for SF (AKA ART)
** See ([http://amigo.berkeleybop.org/cgi-bin/amigo/xp_term_request])
** Could this be better done in wiki?
= Deferred features =


* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
= Known issues =
* 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])
* Migrate peripheral pages to new framework (ongoing)
* Migrate core pages over to the new framework (ongoing)
* 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 ==
Please see the [https://sourceforge.net/tracker/?group_id=36855&atid=908269 tracker].
 
* 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)
 
[[Category:Software]]
[[Category:AmiGO]]

Latest revision as of 17:56, 22 May 2014

Status

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.