AmiGO 1 8: Difference between revisions
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Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. | Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. | ||
= | = Features = | ||
* Centralized testing ([http://amigo.berkeleybop.org/cgi-bin/amigo/page_test?mode=kappa_results kappa]) | * Centralized 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]) | |||
= Current work = | = Current work = | ||
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== Bugs == | == 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 | = Experimental features = | ||
* 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) | * Integrate new RG views from Sven (likely deferred) ([http://amigo.berkeleybop.org/cgi-bin/amigo/phylotree]) | ||
** Check licensing of JS tree viewer | ** Check licensing of JS tree viewer ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=ntree]) | ||
* Relation filtering | * 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 | = Deferred features = | ||
* | * 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]) | |||
* 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://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] | ** [http://berkeleybop.org/alpha/goxprod/go.cgi xprods in 1.6] | ||
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**** [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 TAZ orthoset] (notice heart in top right corner) | **** [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 TAZ orthoset] (notice heart in top right corner) | ||
== TBD | == Plans and TBD == | ||
* | * 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). | * Expand the scope of community annotation (depending on user feedback). | ||
* Switch TE caching over from page render caching to data caching (currently evaluating sqlite3) | * Switch TE caching over from page render caching to data caching (currently evaluating sqlite3) |
Revision as of 18:12, 29 April 2010
Status
Currently experimental.
Features
Current work
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)
- 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
- Matrix tool (nmatrix)
- Integrate new RG views from Sven (likely deferred) ([2])
- Check licensing of JS tree viewer ([3])
- Relation filtering (may be bumped to deferred)
- Start with term enrichment and work out
- Term request client for SF (AKA ART)
- See ([4])
- Could this be better done in wiki?
Deferred features
- Coannotation (possible coannotation interface)
- Advanced graph visualizations [5] [6]
- Early plugin framework done
- Heatmap and random plugin examples
- Workspaces, generalization of sessions (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 (concept)
- xprods in 1.5
- xprods in 1.6
- Examples (all using experimental bp_xp_mouse_anatomy xps):
- heart
- heart development
- TAZ orthoset (notice heart in top right corner)
- Examples (all using experimental bp_xp_mouse_anatomy xps):
Plans and TBD
- 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)