From dstaines at ebi.ac.uk Tue Jan 3 22:28:57 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 03 Jan 2012 22:28:57 +0000 Subject: [ensembl-announce] Ensembl Genomes release 12 biomaRt availability In-Reply-To: <2C40E43D1F7A56408C4463FD245DDDF994ECC06C@EXCHMB-02.stowers-institute.org> References: <2C40E43D1F7A56408C4463FD245DDDF994ECC06C@EXCHMB-02.stowers-institute.org> Message-ID: <4F038129.3000300@ebi.ac.uk> 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/ -- 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/ From dstaines at ebi.ac.uk Tue Jan 3 22:28:57 2012 From: dstaines at ebi.ac.uk (Dan Staines) Date: Tue, 03 Jan 2012 22:28:57 +0000 Subject: [ensembl-announce] Ensembl Genomes release 12 biomaRt availability In-Reply-To: <2C40E43D1F7A56408C4463FD245DDDF994ECC06C@EXCHMB-02.stowers-institute.org> References: <2C40E43D1F7A56408C4463FD245DDDF994ECC06C@EXCHMB-02.stowers-institute.org> Message-ID: <4F038129.3000300@ebi.ac.uk> 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/ -- 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/