AmiGO 1 6 (Archived): Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 7: Line 7:
== Community annotation ==
== Community annotation ==


* Round trip through GONUTS: [http://ash.lbl.gov/cgi-bin/amigo/term-details.cgi?term=GO:0035194]
* Round trip through GONUTS: [http://ash.lbl.gov/cgi-bin/amigo/term-details.cgi?term=GO:0035194 test page]
** AmiGO checks whether the GONUTS wiki has any information about this term, and shows a link to the appropriate GONUTS page if so.  
** AmiGO checks whether the GONUTS wiki has any information about this term, and shows a link to the appropriate GONUTS page if so.  
** Real-time participation
** Real-time participation
Line 34: Line 34:
* site optional links to beta features
* site optional links to beta features


= Current work =


== Other ==
See [[AmiGO 1 7]] for information about the next release.


* most new features make use of the new DBIx::Class-based API on a CGI::Application base
** 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 ==
* Organizing annotation results by qualifier
* 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) ==
* Coannotation
* 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?)


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

Revision as of 15:02, 23 March 2009

Status

Currently beta

New Features

Community annotation

  • Round trip through GONUTS: test page
    • AmiGO checks whether the GONUTS wiki has any information about this term, and shows a link to the appropriate GONUTS page if so.
    • Real-time participation

Reference Genome Support

  • Includes full support for Reference Genome displays
    • Links in from AmiGO
      • gene product search page [1] (search for "pou5f")
      • gene product details page [2]
    • Details [3]
      • details of evidence type
      • sortable
    • Vizualizations
      • Cachable
      • Interative SVG [4]
        • information from the details page
      • Static PNG [5]
    • Summary [6]
      • Cachable
      • evidence type groups

Other (may be changed for final)

  • software page [7]
  • site optional links to beta features


See AmiGO 1 7 for information about the next release.

Retrieved from "https://wiki.geneontology.org/index.php?title=AmiGO_1_6_(Archived)&oldid=18875"