[Bioc-devel] Ensembl Genomes release 12 biomaRt availability

Cook, Malcolm MEC at stowers.org
Tue Jan 3 19:01:00 CET 2012


I am hoping to access the latest S. pombe biomart (http://fungi.ensembl.org/biomart/martview/) using the R wrapper library "biomaRt" 

I believe the mart must be registered with the biomart service registry for this to be possible, but, currently I don't see fungi_mart_12 or fungi_sequence_mart_12 among  http://www.biomart.org/biomart/martservice?type=registry

Since I'm unsure where lies the responsibility for this, I'm cc:ing mart-dev and the biomaRt package developer in this inquiry.

Can someone you please advise when or whether this latest S Pombe will be registered with biomart?  

And, perhaps there is an interim workaround allowing me to use bioconductor's  biomaRt package with this resource in absence of it being registered?

Cheers and Thanks,

~Malcolm Cook

> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On
> Behalf Of Dan Staines
> Sent: Saturday, December 24, 2011 7:15 AM
> To: Giulietta
> Cc: announce at ensembl.org; dev at ensembl.org; eg_internal at ebi.ac.uk
> Subject: Re: [ensembl-dev] [Eg_internal] Ensembl Genomes release 12
> On 12/16/2011 02:48 PM, Giulietta wrote:
> >
> > /Note, EG 12 will be available on ftp next week./
> We are happy to announce the availability of FTP data for EG12, and
> apologise for the late running of this service.
> Seasons greetings,
> Dan.
> --
> 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/
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