query gramene from biomaRt package
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Tine Casneuf ▴ 80
@tine-casneuf-1773
Last seen 7.1 years ago
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
Arabidopsis thaliana Arabidopsis thaliana • 792 views
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sdurinck ▴ 40
@sdurinck-1480
Last seen 7.1 years ago
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. 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
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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 ---------------------------------------------------------------------- -- -------
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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
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