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

[Dan Bolser]

My thinking was that the DASWiki approach could also support the DAS
writeback extension.

On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela
<gsalazar at cs.uct.ac.za> wrote:
> Hello There,
>
> I have been working in an extension to DAS1.6 called
> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow
> to create new versions of an existing feature. So, putting new notes into a
> feature is just a creation of a new version of the feature. The server
> implementation of the writeback extends MyDas
> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk
> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource).
> We are close to release the plugin for Dasty3 to use the writeback server,
> however this first client is a protein client, and so far there is not a
> development for a genome client with DAS writeback capability, but I am
> quite interested in this.
> I hope to be able to announce the release of the writeback client in Dasty3
> in a few days, so you will be able to see it working and see if this
> approach goes in the same direction of what you are looking for.
>
> Regards,
>
> Gustavo.
>
> 2010/10/29 Dan Bolser <dan.bolser at gmail.com>
>>
>> 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)
>> >
>> >
>> > ------------------------------------------------------------------------------
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>> >
>>
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>
>
> --
> Gustavo Adolfo Salazar Orejuela
>