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