[Biojava-dev] Direct access to public genome databases

[Charles Danko]

DAS looks just wonderful, and I am very glad to be made aware of it –
it seems like a much better solution than my initial, highly naive
reaction (accessing public SQL connections).

As I understand it, the easiest way to access DAS services in Java is
via an API such as JAX-WS?   Jumping into the Javadocs, and looking
over a JAX-WS tutorial that I found here:
http://java.sun.com/webservices/docs/2.0/tutorial/doc/ it looks there
is a lot to this.

In this sense, a BioJava class that that takes care of much of the
connecting, data transfer, and parsing would be a welcome convenience
for users not already familiar with this API (like me :).  Even for
those who are well-versed in all of this, such a class would allow DB
access with a lot less code.  Given the frequency that most of us
accesses these public databases, this seems like a worthy goal to me!!

Since its so easy to understand the basics of constructing a DAS
request URL, even something as simple as a class that takes a
pre-formed URL (in the constructor) and acts as an iterator over
whatever information is in the result, would be very useful.

Best,
Charles

On Jan 24, 2008 3:40 AM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
> Hi,
>
> >> Direct access to public genome databases (i.e. a class to import
> >> sequence, annotations, etc. and create the applicable biojava object)
> >> would be a very useful addition to BioJava.  The Ensj project doesn't
> >> look like it has been updated since official support was dropped.  Are
> >> there any plans to work these features into BioJava?  Have I missed
> >> features that already exist?
> >>
> >> Depending on the amount of time required, I may be willing to
> >> contribute to such an endeavor -- particularly for the purpose of
> >> importing sequence.  I have quite a bit of experience working with
> >> java, but not much in a collaborative environment.
> >
>
> Ensembl provides access to more and more of its data via DAS,
> the Distributed Annotation System. DAS is a RESTful protocol to
> access data from distributed sites over the internet.
>
> http://www.ensembl.org/info/using/external_data/das/ensembl_das.html
>
> it is quite heavily used and to see a list of available DAS services
> see
> http://www.dasregistry.org
>
> Andreas
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>