[DAS] [Gmod-gbrowse] Adding comments to a gbrowse database

[Andy Jenkinson]

We also run a simple ProServer SourceAdaptor to pull in content from SNPedia, using the Perlwikipedia CPAN module.

The solution of sending a user to a wiki sounds somewhat clunky to me, but would be relatively easy to set up I imagine. As Gustavo says, a full implementation of writeback in a production system from client through to backend is very close. Dasty3 (client) will be able to edit features directly in the interface, with the edits being stored in a DAS source separate from the original feature.

Something similar could certainly be implemented for GBrowse, but would require development work. But as compensation, no development of the backend would be required.

Cheers,
Andy

On 29 Oct 2010, at 09:55, Dan Bolser wrote:

> Hi Bob,
> 
> This is a nice idea. In my spare time I've been working on running a
> DAS server from a MediaWiki data source. (MediaWiki is the wiki that
> runs Wikipedia).
> 
> In theory, you could have a comments track that was pulled in from the
> 'DASWiki', and clicking the details link would take you to the wiki
> page to edit the comment. Going back to the GBrowse, you would then
> see the updated data from the wiki page. It wouldn't be too hard to
> have a similar workflow for adding new comments.
> 
> I saw a talk from some people at KeyGene who are doing something
> similar (loading DAS into a wiki and linking it to GBrowse to generate
> query reports for specific regions). You can see the talk here:
> 
> SMWCon Fall 2010 / Sunday / Rudi van Bavel
> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program
> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g
> ** http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv
> 
> 
> If anyone wants to take what I have done so far, my (sadly neglected)
> prototype is here:
> 
> http://das.referata.com/wiki/Main_Page
> 
> 
> Kick me a few times and I'll get the underlying code into shape. A
> year or two back I did have a working prototype based on a MediaWiki
> ProServer adaptor.
> 
> 
> If you are interested in community annotation should think about attending this:
> 
> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis:
> http://www.nettab.org/2010/
> 
> 
> Cheers,
> Dan.
> 
> On 26 October 2010 20:31, Bob Muller <bmuller at stanford.edu> wrote:
>> We are working with a small research project that doesn't have funds for a full-scale database for features, so they want to know:
>> 
>> How difficult would it be to add a comment section editable by users to gbrowse?  When you click on a feature in gbrowse it shows a detail page for that feature, is there any way we could enable edits that could be written back to the underlying mysql database that gbrowse runs on?
>> 
>> Their idea is to use the SeqFeature::Store database to hold "comments" entered through GBrowse as a way to annotate their genome. I'd be interested in whether this is possible in GBrowse 1.7 or in 2.x.
>> 
>>   --Bob Muller, TAIR (www.arabidopsis.org)
>> 
>> ------------------------------------------------------------------------------
>> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
>> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> http://p.sf.net/sfu/nokia-dev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das