AmiGO 1 8: Difference between revisions

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


In discussion--currently this is a close descendant of 1.7.
Currently in [http://amigo1.geneontology.org production] (as of 20013-10-17).
 
Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental].
 
= Planned Features =


* TBD...
See [[AmiGO 2]] for the future beta.


= Done 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])
* 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])
* Speed--new caching sub-system for several components (see above for example)


= Current work =
= New experimental (beta) features =


== Future work in progress (visible in live experimental) ==
* [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]).
 
* Switch over to Lucene for searching
** Addition of ubiquitous completion in boxes
* 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 (may be deferred) ([http://amigo.berkeleybop.org/cgi-bin/amigo/phylotree phylotree])
== Planned features ==
** 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)
* Redo of term info/tree view in all locations
** Neighborhood-based view
* Relation filtering
** Start with term enrichment and work out
** 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 ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=front_page 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)
** [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)
== TBD ==


* 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])
* 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]]
Please see the [https://sourceforge.net/tracker/?group_id=36855&atid=908269 tracker].
[[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.