AmiGO 1 7 (Archived): Difference between revisions

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= Status =
= Status =


Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental].
See [[AmiGO 1 8]] for information about the current production release.


= Planned Features =
= New Features =


TBD
== Support for IEAs ==


= Done Features =
All features support the database generated with the IEA subset.


* new/easy graphviz-style graph generation [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=visualize]
== New Graphics Backend ==
** RESTful API (as yet unpublished)
 
** basic and advanced inputs ([[AmiGO_Manual:_Visualize]])
All of the graphics in AmiGO are now handled by a common, and more flexible, backend. Not only does this mean more consistency in the output on different pages, but gives the user the ability to make arbitrary [http://amigo.geneontology.org/cgi-bin/amigo/amigo?mode=visualize custom graphs].
** all graph displays backed by same backend
 
** interactive and static everywhere
=== Details ===
*** term enrichment
*** browser
*** homolset
*** visualize client
* Google analytics throughout AmiGO and associated sites
** optional file to add tracking
** now used on AmiGO Labs, rehomed GOOSE, news4go
* Basic lucene index generation
* OpenSearch [[AmiGO_Manual:_OpenSearch]]
** gene product and term completion suggestions in web browser
** direct access jump or search
** available on Firefox Add-Ons site


= Current work =
* all graph displays backed by same service
* basic and advanced inputs for user client ([[AmiGO_Manual:_Visualize]])
* interactive and static everywhere
** term enrichment
** browser
** homolset
** visualize client
* RESTful API (unpublished)


== Deferred features ==
== Google Analytics ==


* Organizing annotation results by qualifier
The Google analytics code is now throughout AmiGO, AmiGO Labs, and GOOSE. This tracking is enabled with an optional file.
* 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)
** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/go.cgi xprods in 1.5]
** [http://berkeleybop.org/alpha/goxprod/go.cgi xprods in 1.6]
***Examples (all using experimental bp_xp_mouse_anatomy xps):
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-assoc.cgi?term=MA:0000072 heart]
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-details.cgi?term=GO:0007507&session_id=159amigo1208881634 heart development]
**** [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 TAZ orthoset] (notice heart in top right corner)


== Future work in progress (visible in live experimental) ==
== Miscellaneous ==


* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
* Bugs fixed, text repaired (see bug tracker)
* More Lucene ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=lexical_search concept page])
* Little improvements (see request tracker)
** speed
* GOOSE has a new home
** complex search
*** boolean
*** distance
*** weight
** graph information as well?
* advanced graph visualizations [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers_graph] [http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=layers2_graph]
** early plugin framework done
** heatmap and random plugin examples
* bi-ax test [http://toy.lbl.gov:9012/cgi-bin/amigo2/bxdemo] (defunct?)
* Workspaces (generalization of session)


== TBD ==
= Labs (experimental) =


* Expand the scope of community annotation (depending on user feedback).
* Basic lucene index generation
* Switch caching over from page render caching to data caching (currently evaluating sqlite3)
* OpenSearch [[AmiGO_Manual:_OpenSearch]]
* RSS update on terms and gps (could be tied to GONUTs for timeliness?)
** available on Firefox and IE Add-Ons sites
* 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))
** dashboard widget available for Mac OS X
** look at ways of solving "*ase" problem(if it is) (e.g. reverse indexing and merge results)
* JavaScript API core
* OpenLayers-based graph browser
* Live search
* Workspace environment core
* Arbitrarily attachable autocomplete


[[Category:Software]]
[[Category:Software]]
[[Category:AmiGO]]
[[Category:AmiGO]]

Latest revision as of 09:51, 13 December 2018

Status

See AmiGO 1 8 for information about the current production release.

New Features

Support for IEAs

All features support the database generated with the IEA subset.

New Graphics Backend

All of the graphics in AmiGO are now handled by a common, and more flexible, backend. Not only does this mean more consistency in the output on different pages, but gives the user the ability to make arbitrary custom graphs.

Details

  • all graph displays backed by same service
  • basic and advanced inputs for user client (AmiGO_Manual:_Visualize)
  • interactive and static everywhere
    • term enrichment
    • browser
    • homolset
    • visualize client
  • RESTful API (unpublished)

Google Analytics

The Google analytics code is now throughout AmiGO, AmiGO Labs, and GOOSE. This tracking is enabled with an optional file.

Miscellaneous

  • Bugs fixed, text repaired (see bug tracker)
  • Little improvements (see request tracker)
  • GOOSE has a new home

Labs (experimental)

  • Basic lucene index generation
  • OpenSearch AmiGO_Manual:_OpenSearch
    • available on Firefox and IE Add-Ons sites
    • dashboard widget available for Mac OS X
  • JavaScript API core
  • OpenLayers-based graph browser
  • Live search
  • Workspace environment core
  • Arbitrarily attachable autocomplete