AmiGO 1 7 (Archived): Difference between revisions

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= Status =
= Status =


Currently [http://ash.lbl.gov/cgi-bin/amigo/go alpha].
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.


* easy graph generation [http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=visualize]
== New Graphics Backend ==
** RESTful API (as yet unpublished)
** basic and advanced inputs ([[AmiGO_Manual:_Visualize]])
** all graph displays backed by same backend
** interactive and static everywhere
*** term enrichment
*** browser
*** homolset
*** visualize client


= Current work =
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].


== Deferred features ==
=== Details ===


* Organizing annotation results by qualifier
* all graph displays backed by same service
* Term request client for SF (AKA ART)
* basic and advanced inputs for user client ([[AmiGO_Manual:_Visualize]])
** could this be better done in wiki?
* interactive and static everywhere
* Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
** term enrichment
** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/go.cgi xprods in 1.5]
** browser
** [http://berkeleybop.org/alpha/goxprod/go.cgi xprods in 1.6]
** homolset
***Examples (all using experimental bp_xp_mouse_anatomy xps):
** visualize client
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-assoc.cgi?term=MA:0000072 heart]
* RESTful API (unpublished)
**** [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 beta) ==
== Google Analytics ==


* Coannotation (possible [http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
The Google analytics code is now throughout AmiGO, AmiGO Labs, and GOOSE. This tracking is enabled with an optional file.
* OpenSearch
** term completion and suggestions in web browser
** direct access or search
* Lucene ([http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=lexical_search concept page])
** speed
** complex search
*** boolean
*** distance
*** weight
** graph information as well?
* advanced graph visualizations [http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=layers_graph] [http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=layers2_graph]
* bi-ax test [http://toy.lbl.gov:9012/cgi-bin/amigo2/bxdemo] (defunct?)
* Workspaces (generalization of session)


== TBD ==
== Miscellaneous ==


* Expand the scope of community annotation (depending on user feedback).
* Bugs fixed, text repaired (see bug tracker)
* Switch caching over from page render caching to data caching (currently evaluating sqlite3)
* Little improvements (see request tracker)
* RSS update on terms and gps (could be tied to GONUTs for timeliness?)
* GOOSE has a new home
* add Google analytics throughout AmiGO and associated 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))
= Labs (experimental) =
** look at ways of solving "*ase" problem(if it is) (e.g. reverse indexing and merge results)
 
* 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
 
[[Category:Software]]
[[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