AmiGO 1 8: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(New page: = Status = In discussion--currently this is just a copy of 1.7 Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. = Planned Features = TBD = Done Features = * ne...)
 
No edit summary
 
(82 intermediate revisions by 2 users not shown)
Line 1: Line 1:
[[Category:Software]]
[[Category:AmiGO]]
= Status =
= Status =


In discussion--currently this is just a copy 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
 
= Done Features =


* new/easy graphviz-style graph generation [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=visualize]
See [[AmiGO 2]] for the future beta.
** RESTful API (as yet unpublished)
** basic and advanced inputs ([[AmiGO_Manual:_Visualize]])
** all graph displays backed by same backend
** interactive and static everywhere
*** term enrichment
*** browser
*** homolset
*** visualize client
* Google analytics throughout AmiGO and associated sites
** optional file to add tracking
** now used on AmiGO Labs, rehomed GOOSE, news4go
* Basic lucene index generation
* OpenSearch [[AmiGO_Manual:_OpenSearch]]
** gene product and term completion suggestions in web browser
** direct access jump or search
** available on Firefox Add-Ons site


= Current work =
= New features =


== Deferred features ==
* 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])
* 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)


* Organizing annotation results by qualifier
= New experimental (beta) features =
* 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)


== 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]).
* 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])
** 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)
** Start with term enrichment and work out


* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
= Known issues =
* More Lucene ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=lexical_search concept page])
** speed
** complex search
*** boolean
*** distance
*** weight
** graph information as well?
* advanced graph visualizations [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers_graph] [http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=layers2_graph]
** early plugin framework done
** heatmap and random plugin examples
* bi-ax test [http://toy.lbl.gov:9012/cgi-bin/amigo2/bxdemo] (defunct?)
* Workspaces (generalization of session)


== TBD ==
Please see the [https://sourceforge.net/tracker/?group_id=36855&atid=908269 tracker].
 
* Expand the scope of community annotation (depending on user feedback).
* Switch 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.