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.


= New Features =
= New Features =


TBD
== Support for IEAs ==


= Current work =
All features support the database generated with the IEA subset.


== Other ==
== New Graphics Backend ==


* most new features make use of the new DBIx::Class-based API on a CGI::Application base
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].
** 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 ==
=== 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]])
* Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
* interactive and static everywhere
** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/go.cgi xprods in 1.5]
** term enrichment
** [http://berkeleybop.org/alpha/goxprod/go.cgi xprods in 1.6]
** browser
***Examples (all using experimental bp_xp_mouse_anatomy xps):
** homolset
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-assoc.cgi?term=MA:0000072 heart]
** visualize client
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-details.cgi?term=GO:0007507&session_id=159amigo1208881634 heart development]
* RESTful API (unpublished)
**** [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
** 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 =
== Miscellaneous ==


== Client-side ==
* Bugs fixed, text repaired (see bug tracker)
* Little improvements (see request tracker)
* GOOSE has a new home


* Expand the scope of community annotation (depending on user feedback).
= Labs (experimental) =


== Server-side ==
* 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


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