[DAS] Retrieving feature information

[Thomas Down]

I'd have to agree with Lincoln on this one.  The price of being
distributed is that clients have to have the relevant data-integration
smarts.  Unless we're prepared to give up on the premise of 
preserving annotation across changes in the genome assembly,
the current patterns need to stay.

A possible solution to this would be some kind of `projecting proxy'
server, which offers a view of some annotation server mapped onto
the current assembly.  This would actually be relatively easy to
implement using the BioJava DAS client and Dazzle server.  I'm happy
to collaborate with anyone who wants to deploy something like this.

[The caveat, though, is that we might have to be careful about
users hammering this proxy with lots of large requests].

For anyone implementing a programmatic client, however simple,
I'd urge them to connect to `proper' DAS servers and handle the
assembly mapping on the client side.  Java programmers will find
that the org.biojava.bio.program.das library makes this quite easy.
I believe that comparable functionality is available in Perl.

       Thomas.

On Tue, Aug 06, 2002 at 01:05:48PM -0400, Lincoln Stein wrote:
> The reference server could do the coordinate translation, but the annotation 
> servers cannot.  This is because the annotation servers do not necessarily 
> have an up to date version of the assembly.
> 
> The Dazzle Java library handles the coordinate translation for you, so if you 
> use that library, you do not need to worry about the hierarchical traversal.  
> 
> Lincoln
> 
> On Wednesday 31 July 2002 05:05 am, Oliver Lyttelton wrote:
> > Dear Developers,
> >     Please consider this plea, it is heartfelt.
> >
> > When I first heard about DAS, I was in a lecture at Imperial College on
> > distributed Bioinformatics. The concept seemed perfect, the idea of
> > allowing anyone with annotations to publish them in a standard format,
> > which a single genome browser could interpret, creating a virtual free
> > market on the internet, and thus improving the quality of annotation
> > information for everyone.
> >
> > Since I have been using the system, I have come across one massive problem
> > with it, and that is the problem that there is no server-side conversion of
> > coordinate systems during feature requests.
> >
> > I understand the reason for wanting to store features at the lowest (and
> > therefore most stable) level of granularity. However, I fail to see why
> > this prevents real-time server-side conversion.
> >
> > My basic premise is that a "dumb user" such as myself, ought to be able to
> > query (programatically) a DAS annotation server in the coordinate system of
> > their choice, and retrieve a list of all annotations stored on that server,
> > in the same coordinate system. At the moment the amount of conversion
> > required is prohibitive.
> >
> > The task for the server is to translate the request location into
> > chromosome coordinates, and then recurse down through the hierarchy picking
> > up feature info at each level and translating it all into the client
> > coordinate system. This strikes me as a server-side type job not client
> > side, and if someone wrote the code once, it would save every client side
> > program from having to do the same job.
> >
> > To prevent queries returning too much info you could limit the number of
> > features returned to a specific number...
> >
> > Let me know what you think,
> >
> > Best regards to everyone,
> >
> > Oliver Lyttelton (MSc Project Imperial College)
> >
> > _________________________________________________________________
> > Send and receive Hotmail on your mobile device: http://mobile.msn.com
> >
> > _______________________________________________
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das

-- 
We wish to thank the many Firewall vendors who have supported our
work to re-enable the innovation that made the Internet great,
without giving up the cellophane fig leaf of security that a Firewall
provides.           -- Gaynor & Bradner, RFC3093