This is indeed a BioMart server side issue and there is nothing we can try
on the  biomaRt end to fix it.
The plant_mart is maintained by Ensembl so you could report this to
helpdesk@ensembl.org or leave a message here:

http://plants.ensembl.org/Help/Contact

Cheers,
Steffen


On Wed, Feb 2, 2011 at 6:54 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> Maybe I'm missing something, but everything about the scenario you
> describe (especially since you are getting errors via their website)
> seems to suggest that this is a problem on the biomart side, right?
>
> Perhaps you should try contacting them to let them now?
>
> Sorry if I misunderstood.
> -steve
>
> On Wed, Feb 2, 2011 at 3:03 AM, Ying Zhu <Ying.Zhu@csiro.au> wrote:
> > Dear Folks,
> >
> > I encountered a problem with Biomart Query via getBM function in biomaRt
> package.
> >
> >>mart <- useMart("plant_mart_7")
> > +mart<-useDataset("vvinifera_eg_gene",mart)
> >
> +getBM(attributes=c("affy_vitis_vinifera","go_molecular_function_id","entrezgene"),filters="affy_grape",
> +values=c("1616932_at","1608265_at","1614550_at","1608133_at","1618459_at"),
> mart=mart)
> > Checking attributes ... ok
> > Checking filters ... ok
> > Error in getBM(attributes = c("affy_vitis_vinifera",
> "go_molecular_function_id",  :
> >  Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Table 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist
> >
> > And it's the same error when using web query of
> http://www.biomart.org/biomart/marview/
> >
> > Serious Error: Error during query execution: Table
> 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist
> > ERROR: caught BioMart::Exception::Database: Error during query execution:
> Table 'plant_mart_7.efg_affy_vitis_vinifera__dm' doesn't exist
> >
> > I checked this configuration page:
> http://www.biomart.org/biomart/martservice?type=configuration&dataset=vvinifera_eg_gene
> > Two different parameters were found, and I reckon the first was wrong.
> > tableConstraint="efg_affy_vitis_vinifera__dm"
> > tableConstraint="vvinifera_eg_gene__efg_affy_vitis_vinifera__dm"
> > It's obvious that the error happened in "martservice" web server.
> > As the file is on the www.biomat.org server, is it possible to fix that
> within biomaRt package in R?
> > Or what do you think is the root problem? I might be wrong to some
> extent.
> > Thanks a lot in advance for anyone could be of kind help and make any
> suggestions.
> > ===================================================
> > Cordially yours,
> > Ying Zhu
> > PostDoctoral Fellow, CSIRO Plant Industry, Adelaide Laboratory
> > Wine Innovation West Building, Hartley Grove, Urrbrae SA
> > PO Box 350, Glen Osmond SA 5064, Australia
> > Facsimile:   +61 8 8303 8601
> > Cellphone: +61 4 0121 3248
> >
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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