Hi Gareth, exactly as Dan says. My apologies https://lists.biomart.org/pipermail/users/2012-March/002515.html
On Fri, Mar 9, 2012 at 2:03 AM, Dan Staines <[email protected]> wrote: > Hi Gareth, > > I suspect you're connecting directly through biomart central, and I don't > think they've repacked/restarted their servers yet, as Arek mentioned a > slight lag due to a reorganisation of their services. I imagine you can > point your biomaRt adaptor directly at the EBI mart servers/dbs (e.g. > bacteria.ensembl.org/biomart/**martview<http://bacteria.ensembl.org/biomart/martview>or > [email protected]:4157**), though I confess this is something I > don't know much about. Maybe someone else can suggest how to modify things > to use EBI directly? > > Best, > > Dan. > > > On 03/08/2012 06:46 PM, Gareth Morgan wrote: > >> Thanks Dan. I guessed that it might have something to do with the new >> Ensembl release. >> However, I can't see bacteria_mart_13 from within R: >> >> listMarts() >>> >> biomart >> version >> 1 ensembl >> ENSEMBL GENES 65 (SANGER UK) >> 2 snp ENSEMBL >> VARIATION 65 (SANGER UK) >> 3 functional_genomics ENSEMBL >> REGULATION 65 (SANGER UK) >> 4 vega >> VEGA 45 (SANGER UK) >> 5 bacteria_mart_12 >> ENSEMBL BACTERIA 12 (EBI UK) >> >> >> mart=useMart("bacteria_mart_**13") >>> >> Error in useMart("bacteria_mart_13") : >> Incorrect BioMart name, use the listMarts function to see which BioMart >> databases are available >> >> >> Any idea how to get at it from R, or when it will be released? >> Cheers, >> Gareth >> >> >> On 03/08/2012 12:14 AM, Dan Staines wrote: >> >>> Hi Gareth, >>> >>> As mentioned in a mail I sent to the list yesterday, we've now released >>> Ensembl Genomes 13, so bacteria_mart_13 has been retired and is no >>> longer available through our mart interface. The db is still there on >>> our public server if you need to use it directly, but there is no change >>> in the data so I'd suggest you change to use v13 instead. >>> >>> Best, >>> >>> Dan Staines. >>> >>> >> > -- > Dan Staines, PhD Ensembl Genomes Technical Coordinator > EMBL-EBI Tel: +44-(0)1223-492507 > Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 > Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ > > ______________________________**_________________ > Users mailing list > [email protected] > https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users> > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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