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

[Gustavo Adolfo Salazar Orejuela]

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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-- 
Gustavo Adolfo Salazar Orejuela