[BioC] query gramene from biomaRt package

[Will Spooner]

I'm afraid that the GrameneMart database exists on old code behind a 
firewall at present. We will be upgrading the code and providing a public 
database in the coming months.

All the best,

Will

On Fri, 23 Jun 2006, Arek Kasprzyk wrote:

>
> On 23 Jun 2006, at 15:49, sdurinck wrote:
>
>> Hi Tine,
>> 
>> The biomaRt package queries a central webservice at EBI to determine
>> which BioMart database is available and how it can access it.  As soon
>> as Gramene is included in this central webservice,  it will be
>> automatically available for use with biomaRt.  You could ask the Gramene
>> developers and developers at http://www.biomart.org to include Gramene
>> in this system.
>> 
>> As long as Gramene is not in this central webservice biomaRt won't
>> detect it.  In this case you could still use the biomaRt package in
>> MySQL mode if there is public MySQL access to the BioMart database,
>> however as far as I know this is not the case for Gramene.
>> 
>> The last option is that you have a local installation of the Gramene
>> BioMart database and use biomaRt in MySQL mode to query it.
>> 
>
> yes Steffen is right. I am cc'ing Will Spooner who is a lead on Gramene 
> development
> so he can comment on the possible timeline for that. Gramene needs to either 
> expose
> public rdbms server or upgrade to 0.4 which would provide access through
> web services. We'll then pick it up on the central server
>
>
> a.
>
>
>
>
>> best,
>> Steffen
>> 
>> 
>> Quoting Tine Casneuf <tineke.casneuf at ebi.ac.uk>:
>> 
>>> Dear all,
>>> 
>>> Has anyone managed to query the gramene database from the biomaRt
>>> package or can anyone point me to documentation on it? I would like
>>> to
>>> search for information on Arabidopsis thaliana which is in the
>>> database.
>>> 
>>> 
>>> Many thanks in advance,
>>> 
>>> Tine
>>> 
>> 
>> 
>> 
>> 
>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>> 
>> 
>
>
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------
>
>
>

---
William Spooner
WormMart Developer