AmiGO 1 6

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Status

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

New Features

Community annotation

Example with posttranscriptional gene silencing by RNA.

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.

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

Example.

Each homolog set now has its own details page in AmiGO. 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

Example SVG.

Example PNG.

Linked from the details pages are two visual graph-based versions of the information. They come in interactive SVG and static PNG 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

Example.

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

Example.

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.

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

Search

Example (search for "pou5f").

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.

Other

Link to AmiGO Labs

Exmaple.

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.

Other Tools

Example.

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.

Wikified Help

Example.

The AmiGO_manual and help pages have now been wikified for lowering the bar to contribution easing the updating process.

Miscellaneous

  • 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