AmiGO 1 8: Difference between revisions
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* TBD... | * TBD... | ||
= Done Features = | = Done Features = | ||
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= Current work = | = Current work = | ||
== Future work in progress (visible in live experimental) == | |||
* Switch over to Lucene for searching | |||
** Addition of ubiquitous completion in boxes | |||
* Redo of term info/tree view in all locations | |||
** Neighborhood-based view | |||
* Relation filtering | |||
** Start with term enrichment and work out | |||
* Revisit reference genome views and pages | |||
** phylogenic tree | |||
* Migrate peripheral pages to new framework | |||
* Migrate core pages over to the new framework | |||
** Front page with completion ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=front_page concept]) | |||
* Matrix tool ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=nmatrix nmatrix]) | |||
== Deferred features == | == Deferred features == | ||
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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 == | ||
* 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] | ||
** early plugin framework done | ** early plugin framework done | ||
** heatmap and random plugin examples | ** 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) | ||
Revision as of 19:04, 23 November 2009
Status
In discussion--currently this is a close descendant of 1.7. Currently experimental.
Planned Features
- TBD...
Done Features
Current work
Future work in progress (visible in live experimental)
- Switch over to Lucene for searching
- Addition of ubiquitous completion in boxes
- Redo of term info/tree view in all locations
- Neighborhood-based view
- Relation filtering
- Start with term enrichment and work out
- Revisit reference genome views and pages
- phylogenic tree
- Migrate peripheral pages to new framework
- Migrate core pages over to the new framework
- Front page with completion (concept)
- Matrix tool (nmatrix)
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)