AmiGO 1 8: Difference between revisions
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= Status = | = Status = | ||
Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. | Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. Expected to move into testing in the next couple of weeks. | ||
= New features = | = New features = |
Revision as of 14:38, 8 June 2010
Status
Currently experimental. Expected to move into testing in the next couple of weeks.
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 viewTry different iconsTry dynamic lines to highlight ancestorsExplore text-based views- Consensus reached, now polishing
- Default count values
- Use caching?
- 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)
[transitioning now; seth is testing] - 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).[Takes a while--will do more work on exp server.]
Bugs
- Slimmer bug [1]
Upload bug[2]Download GAF bug[3]Links and GO.xref_abbs fun[4] [Done.]To be fixed by direct download?[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] 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
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 [5] [6]
- 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)