[Biojava-dev] Direct access to public genome databases

[Mark Schreiber]

Hi -

>From personal experience you can access data from NCBI and KEGG using
their webservice API's and (depending on the result) use the biojava
parsers to return biojava objects.

The question is, should this activity be wrapped into biojava (ie
should the webservice stuff be inside biojava)?

Pros:  Happens behind the scenes, users don't need to know about WS,
possible uniform interface to several sources
Cons: Lots more dependencies on WS jars (take a look at JAX-WS for
example) and WS client jars

I'm interested in hearing more pros and cons from other people. This
is timely given the upcoming webservices meet up in Tokyo.

Best regards,

- Mark


On Jan 23, 2008 8:06 PM, Michael Heuer <heuermh at acm.org> wrote:
> Charles Danko wrote:
>
> > Hello,
> >
> > 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.
>
> What sort of client API would you have in mind?
>
>
> I'm not a Taverna expert, but it seems to me that access to third-party
> data resources is already well covered with the web services available
> there.
>
> > http://taverna.sourceforge.net/
> > http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
>
> Or simply call the web services directly.
>
>    michael
>
>
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