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

[Dan Bolser]

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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