[Bioc-devel] Ensembl Genomes release 12 biomaRt availability

Wolfgang Huber whuber at embl.de
Wed Jan 4 15:50:12 CET 2012

Dear Malcolm

thank you. Once the problem with the Emsembl / biomart.org communication 
is addressed, and if a problem persists at the biomaRt level, please let 
me know. Better even, use the Bioconductor mailing list if the problem 
is likely to be close to the R/Bioconductor layer.

	Best wishes

Dan Staines scripsit 01/03/2012 11:28 PM:
> It looks like our normal post-release mail to the biomart.org people to
> let them know about a new set of marts has not gone through, so I'll
> give them a shout. I can't help you on on a biomaRt workaround though...
> On 01/03/2012 06:01 PM, Cook, Malcolm wrote:
>> Hi,
>> 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/
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe):
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/

Best wishes

Wolfgang Huber

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