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

[Andy Jenkinson]

Hi Dan,

Sounds interesting. How do you see that working?

Cheers,
Andy

On 29 Oct 2010, at 16:28, Dan Bolser wrote:

> 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
>> 
> 
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