AmiGO 1 8: Difference between revisions
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* Try and lighten up on some of the POSTs in AmiGO to make searches easier to track | * 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 | * Finish new term details page--find way to avoid confusion with old view | ||
** Try different icons | ** <strike>Try different icons</strike> | ||
** Try dynamic lines to highlight ancestors | ** <strike>Try dynamic lines to highlight ancestors</strike> | ||
** Explore text-based views | ** Explore text-based views | ||
* Re-expose the buckets in slimmer | * Re-expose the buckets in slimmer | ||
Line 32: | Line 32: | ||
* Upload bug [https://sourceforge.net/tracker/?func=detail&aid=2962252&group_id=36855&atid=908269] | * Upload bug [https://sourceforge.net/tracker/?func=detail&aid=2962252&group_id=36855&atid=908269] | ||
* Download GAF bug [https://sourceforge.net/tracker/?func=detail&aid=2821450&group_id=36855&atid=908269] | * Download GAF bug [https://sourceforge.net/tracker/?func=detail&aid=2821450&group_id=36855&atid=908269] | ||
* Links and GO.xref_abbs fun [https://sourceforge.net/tracker/?func=detail&aid=2996856&group_id=36855&atid=908269] [Done.] | * <strike>Links and GO.xref_abbs fun</strike> [https://sourceforge.net/tracker/?func=detail&aid=2996856&group_id=36855&atid=908269] [Done.] | ||
** To be fixed by direct download? [Yes. 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) | * Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream) | ||
Revision as of 17:24, 12 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 iconsTry 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) [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).
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
- 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)