AmiGO 1 8: Difference between revisions
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*** Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream) | *** Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream) | ||
= | = Experimental features (visible in live experimental) = | ||
* Addition of ubiquitous completion in boxes | * Addition of ubiquitous completion in boxes | ||
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* Integrate new RG views from Sven (likely deferred) | * Integrate new RG views from Sven (likely deferred) | ||
** Check licensing of JS tree viewer | ** Check licensing of JS tree viewer | ||
* Relation filtering | * Relation filtering | ||
** Start with term enrichment and work out | ** Start with term enrichment and work out | ||
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** Front page with completion ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=front_page concept]) | ** Front page with completion ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=front_page concept]) | ||
= Deferred features (stubs and plans) = | |||
* Organizing annotation results by qualifier | * Organizing annotation results by qualifier | ||
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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 == | == TBD (none of the above) == | ||
* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface) | * Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface) | ||
Revision as of 17:47, 29 April 2010
Status
Currently experimental.
Done 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 (visible in live experimental)
- Addition of ubiquitous completion in boxes
- Matrix tool (nmatrix)
- Integrate new RG views from Sven (likely deferred)
- Check licensing of JS tree viewer
- Relation filtering
- Start with term enrichment and work out
- Migrate peripheral pages to new framework
- Migrate core pages over to the new framework
- Front page with completion (concept)
Deferred features (stubs and plans)
- 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)
- 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):
TBD (none of the above)
- Coannotation (possible coannotation interface)
- Advanced graph visualizations [1] [2]
- Early plugin framework done
- Heatmap and random plugin examples
- Workspaces, generalization of sessions (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)