AmiGO 1 8: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(New page: = Status = In discussion--currently this is just a copy of 1.7 Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. = Planned Features = TBD = Done Features = * ne...)
 
No edit summary
Line 1: Line 1:
= Status =
= Status =


In discussion--currently this is just a copy of 1.7
In discussion--currently this is a close descendant of 1.7.
 
Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental].
Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental].


= Planned Features =
= Planned Features =


TBD
* TBD...
* ...
* ...


= Done Features =
= Done Features =


* new/easy graphviz-style graph generation [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=visualize]
* Centralized testing (http://amigo.berkeleybop.org/cgi-bin/amigo/page_test?mode=kappa_results)
** RESTful API (as yet unpublished)
* GOOSE integrated into framework
** basic and advanced inputs ([[AmiGO_Manual:_Visualize]])
** all graph displays backed by same backend
** interactive and static everywhere
*** term enrichment
*** browser
*** homolset
*** visualize client
* Google analytics throughout AmiGO and associated sites
** optional file to add tracking
** now used on AmiGO Labs, rehomed GOOSE, news4go
* Basic lucene index generation
* OpenSearch [[AmiGO_Manual:_OpenSearch]]
** gene product and term completion suggestions in web browser
** direct access jump or search
** available on Firefox Add-Ons site


= Current work =
= Current work =
Line 46: Line 32:
== Future work in progress (visible in live experimental) ==
== Future work in progress (visible in live experimental) ==


* Matrix tool ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=nmatrix nmatrix])
* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
* More Lucene ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=lexical_search concept page])
* Lucene as general search ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=lexical_search concept page])
** speed
** complex search
*** boolean
*** distance
*** weight
** graph information as well?
** graph information as well?
* advanced graph visualizations [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers_graph] [http://ash.lbl.gov/cgi-bin/amigo/amigo_exp?mode=layers2_graph]
* advanced graph visualizations [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers_graph] [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers2_graph]
** early plugin framework done
** early plugin framework done
** heatmap and random plugin examples
** heatmap and random plugin examples
* bi-ax test [http://toy.lbl.gov:9012/cgi-bin/amigo2/bxdemo] (defunct?)
* Workspaces, generalization of sessions ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=workspace_client concept])
* Workspaces (generalization of session)


== TBD ==
== TBD ==


* Expand the scope of community annotation (depending on user feedback).
* Expand the scope of community annotation (depending on user feedback).
* Switch caching over from page render caching to data caching (currently evaluating sqlite3)
* Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)
* RSS update on terms and gps (could be tied to GONUTs for timeliness?)
* RSS update on terms and gps (could be tied to GONUTs for timeliness?)
* 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))
* 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))
** look at ways of solving "*ase" problem(if it is) (e.g. reverse indexing and merge results)
** look at ways of solving "*ase" problem (if it is) (e.g. reverse indexing and merge results)


[[Category:Software]]
[[Category:Software]]
[[Category:AmiGO]]
[[Category:AmiGO]]

Revision as of 18:06, 23 November 2009

Status

In discussion--currently this is a close descendant of 1.7. Currently experimental.

Planned Features

  • TBD...
  • ...
  • ...

Done Features

Current work

Deferred features

  • Organizing annotation results by qualifier
  • Term request client for SF (AKA ART)
    • could this be better done in wiki?
  • Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)

Future work in progress (visible in live experimental)

  • Matrix tool (nmatrix)
  • Coannotation (possible coannotation interface)
  • Lucene as general search (concept page)
    • graph information as well?
  • advanced graph visualizations [1] [2]
    • early plugin framework done
    • heatmap and random plugin examples
  • Workspaces, generalization of sessions (concept)

TBD

  • Expand the scope of community annotation (depending on user feedback).
  • Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)
  • RSS update on terms and gps (could be tied to GONUTs for timeliness?)
  • 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))
    • look at ways of solving "*ase" problem (if it is) (e.g. reverse indexing and merge results)
Retrieved from "https://wiki.geneontology.org/index.php?title=AmiGO_1_8&oldid=22995"