AmiGO 1 6 (Archived): Difference between revisions

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* beta planned for early July
= Status =


== Reference Genome Support ==
Currently [http://ash.lbl.gov/cgi-bin/amigo/go beta]
 
== Community annotation ==


* AmiGO 1.6 exp top [http://accordion.lbl.gov/cgi-bin/amigo/amigo]
* Round trip through GONuts.
** moving refG homolset summary into AmiGO framework [DONE]
* Real-time participation
** moving refG homolset comparison graphs into AmiGO framework [DONE]
* display of homolsets on gene pages from AmiGO (tying) [search/detail--DONE]
* better reporting of homolset information (integration of reports)
* organizing annotation results by qualifier


== Other ==
== Reference Genome Support ==


* AmiGO 1.6 bi-ax test [http://toy.lbl.gov:9012/cgi-bin/amigo2/bxdemo]
* Includes full support for Reference Genome displays
* Round trip with GONUTS [AmiGO half--DONE]
** Links in from AmiGO
*** gene product search page
*** gene product details page
** Details
*** sortable
** Vizualizations
*** Cachable
*** Interative SVG
*** Static PNG
** Summary
*** Cachable


== Cross-product and inter-ontology link support ==
== Deferred features ==


(may be punted until following release, but we will start on necessary infrastructure changes)
* Organizing annotation results by qualifier
* Term request client
* 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)


* [http://toy.lbl.gov:9012/cgi-bin/go_xprod/go.cgi xprods in 1.5]
== Other ==
* [http://berkeleybop.org/alpha/goxprod/go.cgi xprods in 1.6]


Examples:
* most new features make use of the new DBIx::Class-based API
**
* first use of automated web testing (tanuki)
** tens of thousands page visits
** caught a fair number of bad links


(all using experimental bp_xp_mouse_anatomy xps)
== Future work ==


* [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-assoc.cgi?term=MA:0000072 heart]
* Qualifiers in display
* [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-details.cgi?term=GO:0007507&session_id=159amigo1208881634 heart development]
* Term request client to SF
* [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 TAZ orthoset] (notice heart in top right corner)
* Lucene
** complex search
*** boolean
*** distance
*** weight
** graph information as well?
* AmiGO 1.6 bi-ax test [http://toy.lbl.gov:9012/cgi-bin/amigo2/bxdemo] (defunct?)


[[Category:Reference Genome]]
[[Category:Reference Genome]]
[[Category:Software]]
[[Category:Software]]
[[Category:AmiGO]]
[[Category:AmiGO]]

Revision as of 20:09, 17 October 2008

Status

Currently beta

Community annotation

  • Round trip through GONuts.
  • Real-time participation

Reference Genome Support

  • Includes full support for Reference Genome displays
    • Links in from AmiGO
      • gene product search page
      • gene product details page
    • Details
      • sortable
    • Vizualizations
      • Cachable
      • Interative SVG
      • Static PNG
    • Summary
      • Cachable

Deferred features

  • Organizing annotation results by qualifier
  • Term request client
  • Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)

Other

  • most new features make use of the new DBIx::Class-based API
  • first use of automated web testing (tanuki)
    • tens of thousands page visits
    • caught a fair number of bad links

Future work

  • Qualifiers in display
  • Term request client to SF
  • Lucene
    • complex search
      • boolean
      • distance
      • weight
    • graph information as well?
  • AmiGO 1.6 bi-ax test [1] (defunct?)
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