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) | ||
= | = New experimental (beta) 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 ( | * 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]) | ** 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) | * Relation filtering (may be bumped to deferred) | ||
** Start with term enrichment and work out | ** Start with term enrichment and work out | ||
= Deferred (alpha) features = | = Deferred (alpha) features = | ||
* 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) | * 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] | * 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] |
Revision as of 13:36, 3 May 2010
Status
Currently experimental.
New features
- Centralized internal testing (kappa)
- GOOSE integrated into framework (GOOSE)
- Rapid searching (live search)
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
- Bug [1]
- Bug [2]
- GO.xref_abbs fun. (seth--check on current condition)
- 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
- 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
Deferred (alpha) features
- Term request client for SF (AKA ART) (XP term request)
- Could this be better done in wiki?
- Coannotation (possible coannotation interface)
- Advanced graph visualizations [3] [4]
- Early plugin framework done
- Heatmap and random plugin examples
- Workspaces, generalization of sessions (concept)
- 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
- 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)