AmiGO 1 9: Difference between revisions

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[[Category:Software]]
[[Category:AmiGO]]
= Status =
= Status =


On paper.
This has been stopped in favor of [[AmiGO_2 | AmiGO 2.0]].
 
Will soon be at [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental].


* Testing:
* Testing:
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== Frontend==
== Frontend==


* Search
* Search :started:
** Ubiquitous completion
** Ubiquitous completion
** Interface to search index.
** Interface to search index.
** Bump current search to different page.
** Bump current search to different page.
* GP/Term Matrix.
* Make this [http://amigo.berkeleybop.org/cgi-bin/amigo/search.cgi?search_query=xerC&action=new-search&search_constraint=gp] more intuitive--if there are zero annotations then it shouldn't tease you with a link that says "view annotations". [https://sourceforge.net/tracker/?func=detail&aid=3111746&group_id=36855&atid=908269]
* TBD
* TBD


== Backend ==
== Backend ==


* Convert most searches to Solr backend.
* Newick redo :looking:
* Galaxy hooks.
* Better installation for non-GO ontology-only [https://sourceforge.net/tracker/index.php?func=detail&aid=3096652&group_id=36855&atid=908269]
* Newick redo.
* better file filtering on uploads


== Bugs ==
== Bugs ==
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= Experimental (beta) features =
= Experimental (beta) features =
This area is for things that have functioning public code are are planned for inclusion somewhere down the road. AmiGO Labs likely has them.


* Integrate new RG views from Sven (may be deferred) ([http://amigo.berkeleybop.org/cgi-bin/amigo/phylotree phylotree])
* Integrate new RG views from Sven (may be deferred) ([http://amigo.berkeleybop.org/cgi-bin/amigo/phylotree phylotree])
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** Start with term enrichment and work out
** Start with term enrichment and work out


= Deferred (alpha) features =
= Plans and TBD =
 
This area is for things that are still in the planning stage for eventual inclusion, and may or may not have functioning public code. Things in here will hopefully be bumped up or down.
 
* Figure out new framework (ongoing)
** Migrate peripheral pages to new framework (ongoing)
** Migrate core pages over to the new framework (ongoing)
* Term Enrichment
** Species
** Relation filtering (regulates)
* GP/Term Matrix.
* Column 16
* Convert most searches to Solr backend.
** Replace traditional search with lucene-backed
** Everything (except relational case) to consume Solr service
* Slimmer rebuild
* Ditch term-details.cgi completely
** Means a redo of the subset pages
* Trying Galaxy
** Galaxy hooks.
** In and out from AmiGO
** Sessions via local Galaxy install
* Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
* Organizing annotation results by qualifier
* Expand the scope of community annotation (depending on user feedback).
* RSS update on terms and gps (could be tied to GONUTs for timeliness?)
 
= Deferred features =
 
These are features that may or may not have working code checked in, but are not currently planned for any kind of testing or release.


* <strike>Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)</strike> [likely bumped in favor of new tools]
* <strike>Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)</strike> [likely bumped in favor of new tools]
Line 59: Line 90:
**** [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 TAZ orthoset] (notice heart in top right corner)
**** [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 TAZ orthoset] (notice heart in top right corner)


= Plans and TBD =
= Known issues =
 
* Migrate peripheral pages to new framework (ongoing)
* Migrate core pages over to the new framework (ongoing)
* Term Enrichment
** Species
** Relation filtering (regulates)
* Column 16
* Solr (see above)
* Slimmer rebuild
** Replace traditional search with lucene-backed
** Everything to consume Solr service
* Trying Galaxy
** In and out from AmiGO
** Sessions via local Galaxy install
* Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
* Organizing annotation results by qualifier
* Expand the scope of community annotation (depending on user feedback).
* RSS update on terms and gps (could be tied to GONUTs for timeliness?)


[[Category:Software]]
Please see the [https://sourceforge.net/tracker/?group_id=36855&atid=908269 tracker].
[[Category:AmiGO]]
[[Category:Software Progress]]

Latest revision as of 10:16, 25 October 2017

Status

This has been stopped in favor of AmiGO 2.0.

  • Testing:
    • TBD

New features

  • TBD

Current work

Frontend

  • Search :started:
    • Ubiquitous completion
    • Interface to search index.
    • Bump current search to different page.
  • Make this [1] more intuitive--if there are zero annotations then it shouldn't tease you with a link that says "view annotations". [2]
  • TBD

Backend

  • Newick redo :looking:
  • Better installation for non-GO ontology-only [3]
  • better file filtering on uploads

Bugs

  • Slimmer bug [4]

Experimental (beta) features

This area is for things that have functioning public code are are planned for inclusion somewhere down the road. AmiGO Labs likely has them.

  • Integrate new RG views from Sven (may be deferred) (phylotree)
    • Check licensing of JS tree viewer (ntree)
  • Relation filtering (may be bumped to deferred)
    • Start with term enrichment and work out

Plans and TBD

This area is for things that are still in the planning stage for eventual inclusion, and may or may not have functioning public code. Things in here will hopefully be bumped up or down.

  • Figure out new framework (ongoing)
    • Migrate peripheral pages to new framework (ongoing)
    • Migrate core pages over to the new framework (ongoing)
  • Term Enrichment
    • Species
    • Relation filtering (regulates)
  • GP/Term Matrix.
  • Column 16
  • Convert most searches to Solr backend.
    • Replace traditional search with lucene-backed
    • Everything (except relational case) to consume Solr service
  • Slimmer rebuild
  • Ditch term-details.cgi completely
    • Means a redo of the subset pages
  • Trying Galaxy
    • Galaxy hooks.
    • In and out from AmiGO
    • Sessions via local Galaxy install
  • Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
  • Organizing annotation results by qualifier
  • Expand the scope of community annotation (depending on user feedback).
  • RSS update on terms and gps (could be tied to GONUTs for timeliness?)

Deferred features

These are features that may or may not have working code checked in, but are not currently planned for any kind of testing or release.

  • Switch TE caching over from page render caching to data caching (currently evaluating sqlite3) [likely bumped in favor of new tools]
  • Term request client for SF (AKA ART) (XP term request)
    • Could this be better done in wiki?
  • Coannotation (possible coannotation interface)
  • Advanced graph visualizations [5] [6]
    • Early plugin framework done
    • Heatmap and random plugin examples
  • Workspaces, generalization of sessions (concept)
  • Addition of ubiquitous completion in boxes

Known issues

Please see the tracker.

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