[BioC] query gramene from biomaRt package

sdurinck Steffen.Durinck at esat.kuleuven.be
Fri Jun 23 16:49:33 CEST 2006

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.


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

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