AmiGO 1 6 (Archived): Difference between revisions

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A link in the footer has also been added that (indirectly) links to an experimental version of AmiGO in order to get early feedback on new features.
A link in the footer has also been added that (indirectly) links to an experimental version of AmiGO in order to get early feedback on new features.


= Misc. =
* 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 (tanuki)
** 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


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

Revision as of 20:36, 27 March 2009

Status

Currently beta.

See AmiGO 1 7 for information about the release after 1.6.

New Features

Community annotation

Term Information now contains a category for "Community". This reflects the current activity for the term on the GONUTS wiki. In addition, the GONUTS wiki now contains links back into AmiGO, so a user can easily move back and forth between the two. This allows real-time participation for the community.

For more information, please see AmiGO_Manual:_Term_Details#Community.

Example: Round trip through GONUTS: test page

Technical detail: AmiGO checks whether the GONUTS wiki has any information about this term using the GONUTS API.

Reference Genome Support

Several things have been added to AmiGO to support the addition of the Reference Genome information to the GO database.

Details

Each homolog set now has its own details page in AmiGO (for example). These details pages include information about the reference genome annotations to GO terms for all of the reference genome species, as well as the best type of evidence used.

The GO terms are sortable by several criteria.

For more information about the RG details pages, see AmiGO_Manual:_RG_Details.

Technical detail: these pages are cachable on the server side.

Visualizations

Linked from the details pages are two visual graph-based versions of the information. They come in interactive SVG (example) and static PNG (example) formats. These allow the user to more easily digest GO graph information that may not be clear from the text version on the details pages.

For more information about the graphical views, see AmiGO_Manual:_RG_Graphical_View.

Technical detail: these pages are cachable on the server side.

Summary

There is also a summary page that contains a distilled version of the information in the details pages for all homolog sets.

For more information about the summary page, see AmiGO_Manual:_RG_Summary.

Technical detail: this page is cached on the server side.

Links

In order for users to access the new Reference Genome information, when available, gene product details pages have had links to the new homolset information added (example).

For more detailed information, see AmiGO_Manual:_Gene_Product_Details#Ref_Genome.

Search

On gene product search pages, gene product results that have reference genome information connected with them now appear with a '*' next to the gene product name (example) (search for "pou5f").

Other

There has been the addition of an Other Tools button to the toolbar. This links to an overview page of the software available in AmiGO. It is sparsely populated at the moment, but as more tools are added to AmiGO, this will become a major hub.

A link in the footer has also been added that (indirectly) links to an experimental version of AmiGO in order to get early feedback on new features.

Misc.

  • 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 (tanuki)
    • 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