Taverna

On 10 Mar 2006, at 04:25, Twigger Simon wrote:

> Hi there,
>
> I'm using Taverna 1.3.1 on the mac and Im having some problems  
> accessing the standard Biomart dbs at EBI. The Biomart registry listed  
> in Available Processors just has a folder icon, you cant expand the  
> folder and see the available biomart dbs listed. Similarly, when I try  
> to add a new Biomart instance hosted at EBI it silently fails and no  
> biomart appears in the list of available processors.
>
> I was wondering if something is going on behind the scenes or if I  
> should be moving over to the new webservice interface in biomart 0.4  
> (though the old way of configuring a biomart query in taverna was  
> really convenient so I hope its not going away).
>


Hi Simon,
I can't really speak for taverna folks here but as I mentioned in my  
0.4 email
announcement a while back the registry format has been changed with 0.4
As far as I know taverna relies on quite dated martj library and if  
taverna uses
the pointer to the central registry it might be a possible reason.

Try editing your local registry to point to marts directly rather than  
going through
a pointer. There is a chance that this could do the trick.
If you need any help with that please drop us an email off the list and  
we'll
send you an example (I'll have no email contact today so cc'ing Damian  
who would
be able  to help you instead)


a.





> Cheers,
>
> 	Simon.
>
> --
>
> Simon N. Twigger, Ph.D.
> Assistant Professor, Department of Physiology
> Medical College of Wisconsin
> 8701 Watertown Plank Road,
> Milwaukee, WI, USA
> tel: 414-456-8802
> fax: 414-456-6595
> AIM/iChat: simontatmcw
>
>
>


------------------------------------------------------------------------ 
-------
Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
------------------------------------------------------------------------ 
-------

Simon,

We're putting a developer on sorting out Taverna / Biomart integration, 
we haven't had the resources up to this point to track the changes in 
Biomart in a timely fashion. We've had to maintain our own branch of the 
MartJ code so it's not just a question of dropping in a new library but 
this should be eased by the new service interface assuming that remains 
stable (and especially assuming the database metadata formats are stable).

I can't give a precise timeframe on this but we are now actively working 
on getting it sorted out.

Biomart guys - could you maybe produce a paragraph summarizing the 
expected change rate of the various components, so the service, the 
query specification format, the registry mechanisms and the database 
metadata format?

Cheers,

Tom

On Fri, 10 Mar 2006, Tom Oinn wrote:

> Simon,
> 
> We're putting a developer on sorting out Taverna / Biomart integration, 
> we haven't had the resources up to this point to track the changes in 
> Biomart in a timely fashion. We've had to maintain our own branch of the 
> MartJ code so it's not just a question of dropping in a new library but 
> this should be eased by the new service interface assuming that remains 
> stable (and especially assuming the database metadata formats are stable).
> 
> I can't give a precise timeframe on this but we are now actively working 
> on getting it sorted out.
> 
> Biomart guys - could you maybe produce a paragraph summarizing the 
> expected change rate of the various components, so the service, the 
> query specification format, the registry mechanisms and the database 
> metadata format?

this should all be stable now for the forseeable future (at least until 
0_5 release in teh summer). Things like the internal names for attributes 
and filters may vary a bit as we redo configurations but these are 
discoverable through the service interface

cheers
Damian


> 
> Cheers,
> 
> Tom
>