AmiGO 1 7 (Archived): Difference between revisions

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= Current work =
= Status =


== Other ==
See [[AmiGO 1 8]] for information about the current production release.


* most new features make use of the new DBIx::Class-based API on a CGI::Application base
= New Features =
** improved speed
** improved clarity
* first use of automated web testing
** tens of thousands page visits
** caught a fair number of bad links and pages
** small changes in future AmiGO design to support better automated testing


== Deferred features ==
== Support for IEAs ==


* Organizing annotation results by qualifier
All features support the database generated with the IEA subset.
* Term request client for SF
* 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 beta) ==
== New Graphics Backend ==


* Coannotation
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].
* OpenSearch
** term completion and suggestions in web browser
** direct access or search
* Lucene
** speed
** complex search
*** boolean
*** distance
*** weight
** graph information as well?
* advanced graph visualizations
* bi-ax test [http://toy.lbl.gov:9012/cgi-bin/amigo2/bxdemo] (defunct?)


= Wishlists =
=== Details ===


== Client-side ==
* 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* RESTful API (unpublished)


* Expand the scope of community annotation (depending on user feedback).
== Google Analytics ==


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


* Switch caching over from page render caching to data caching (currently evaluating sqlite3)
== Miscellaneous ==
* Change all graph displays to be backed by standard backend (see visualize experimental AmiGO module)
 
*
* 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
 
[[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