[Biojava-dev] Direct access to public genome databases

[Andy Yates]

Andreas Prlic wrote:
> 
>> 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).
> 
> don;t think that this is naive. There is also ensembldb.ensembl.org
> which is a public mysql server if you prefer sql....

I have to agree. There's a lot to be said about using a database 
directly (in fact my group does just that). But it is potentially a more 
fragile solution than using a public api.

>>
>> 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.
> 
> I have not tried JAX-WS yet, so I can not comment on that, but if you 
> want a library
> that makes it easier to talk to DAS servers, you can use my
> DAS client library at: http://www.spice-3d.org/dasobert/

I would stay away from JAX-WS. It's a web services framework which is 
more for SOAP access than anything else. Even when using it for SOAP 
remoting I've found it less than intuitive (maybe later version have 
gotten better about this especially with the Java6 compiler api 
hopefully removing any need for explicit annotation processing). Chances 
are it would be easier to use JAX-WS when the REST service support comes 
in but until then I would say stay away from it.

Andreas' library is a far superior solution :)

Andy