[Gmod-help] Possibility of querying external resources

[Scott Cain]

Hi Nipun,

I'm guessing you're asking about DNA feature annotation (like genes
and the like).  There are a few ways to incorporate data from remote
sources.  There are two primary tools in the GMOD project for doing
this type of work: Apollo and WebApollo.  Apollo has been around for
years and is a desktop Java application for doing graphical feature
annotation.  If you are using that, it is a little less easy to bring
in remote sources--the easiest thing to do is get data dumps from the
remote provider and load it into your Chado instance.  I don't think
you can use something like DAS (distributed annotation system) to
bring data into Apollo directly.

WebApollo on the other hand will likely do the remote source thing
much better, but it is still early in development.  It is based on
JBrowse and will let users edit genome features in a web browser.
Fairly high on their list of things to implement is exactly that, so
when it's ready, I think it will be an excellent tool for this
purpose.  I expect an initial release of WebApollo by the end of the
year.

A stop gap so that you could use Apollo and still provide your users
an integrated view including remote data would be to set up a GBrowse
instance that would pull data both from your local Chado instance as
well as data from remote sources via DAS.  Having two windows is less
than ideal, but isn't terrible.  You can also configure GBrowse so
that when users click on a feature, it will open it in Apollo and
allow them to edit the feature, giving that arrangement some nice
interactivity.  I wrote a demo project doing something like this call
the Community Annotation System (CAS).

Here are wiki pages for both projects, which should lead you to more
information, including mailing lists where you can ask more questions:

  http://gmod.org/wiki/Apollo

  http://gmod.org/wiki/WebApollo

  http://gmod.org/wiki/Community_Annotation_System

Scott


On Thu, Apr 19, 2012 at 8:21 PM, Nipun Mistry <nmistry2 at jhu.edu> wrote:
> Hi,
>
> It was really great to come across GMOD. I am planning to set up a central
> database for scientists who will be sequencing a number of organisms in the
> coming years. I looked up Chado and find it to be great for our needs.
>
> However, we would also need to annotate/map our sequences and use a resource
> for this not on our systems to minimize computational expense. Is it
> possible to query external publicly available websites/resources with the
> desired sequences in our local database for annotation/browsing work? Could
> you guide me or point me to the resources where I can learn to set up such a
> system?
>
> Thanks!
>
> Nipun



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research