Difference between revisions of "AmiGO 1 8"

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= Status =
= Status =
Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. Expected to move into testing in the next couple of weeks.
Currently in [http://amigo1.geneontology.org production] (as of 20013-10-17).
See [[AmiGO 2]] for the future beta.
= New features =
= New features =
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* 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])
* 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==
* <strike>Try and lighten up on some of the POSTs in AmiGO to make searches easier to track</strike>
* Finish new term details page
** <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?</strike> [will check with auto tester]
** Default gp count values
** Fix td downloads
* Re-expose the buckets in slimmer [may be bumped if other reporting can be found]
* 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) <strike>[transitioning now; seth is testing]</strike>
* 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))
* <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.]
* Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)
= New experimental (beta) features =
= New experimental (beta) features =
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** Start with term enrichment and work out
** Start with term enrichment and work out
= Deferred (alpha) features =
= Known issues =
* 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 ==
Please see the [https://sourceforge.net/tracker/?group_id=36855&atid=908269 tracker].
* Migrate peripheral pages to new framework (ongoing)
* Migrate core pages over to the new framework (ongoing)
* 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)

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.