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]. | ||
= Done Features = | = Done Features = | ||
| Line 16: | Line 10: | ||
= Current work = | = Current work = | ||
== Future work in progress (visible in live experimental) == | == 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) | |||
== Future work in progress (sometimes visible in live experimental) == | |||
* Addition of ubiquitous completion in boxes | |||
* 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) | |||
** Check licensing of JS tree viewer | |||
== Planned features == | == Planned features == | ||
* Relation filtering | * Relation filtering | ||
** Start with term enrichment and work out | ** Start with term enrichment and work out | ||
* Migrate peripheral pages to new framework | * Migrate peripheral pages to new framework | ||
* Migrate core pages over to the new framework | * Migrate core pages over to the new framework | ||
| Line 38: | Line 50: | ||
* Organizing annotation results by qualifier | * Organizing annotation results by qualifier | ||
* Term request client for SF (AKA ART) | * 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) | * Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes) | ||
** [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] | ||
| Line 50: | Line 62: | ||
* 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] | ||
** | ** 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]) | * Workspaces, generalization of sessions ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=workspace_client concept]) | ||
* 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) | ||
* RSS update on terms and gps (could be tied to GONUTs for timeliness?) | * 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) | ||
[[Category:Software]] | [[Category:Software]] | ||
[[Category:AmiGO]] | [[Category:AmiGO]] | ||
Revision as of 17:44, 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)
Future work in progress (sometimes 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
Planned features
- 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
- 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
- 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)