[BioC] Access to archived versions of Ensembl with biomaRt

[Cook, Malcolm]

I inquired at Ensemb Helpdesk on this matter a week ago and was told:

	Hello Malcolm,
	No, I am afraid that for Ensembl Genomes we don't make older versions available through an Archive! site, like we do for Ensembl.
	-- 
	With kind regards,
	Bert Overduin, Ph.D.
	(Ensembl Helpdesk)

Sniff?

~Malcolm


> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-
> bounces at r-project.org] On Behalf Of mjonczyk
> Sent: Tuesday, January 10, 2012 2:33 PM
> To: adrcort at gmail.com; bioconductor at r-project.org
> Subject: Re: [BioC] Access to archived versions of Ensembl with biomaRt
> 
> Hi Adrian,
> 
> First of all, I've also seen that something changes. My best advice
> is that you could submit listMarts(), choose the one closest to
> previously used and see if listDatasets() will give you expected
> organisms.
> 
> I've used plant database, some time ago it was "ENSEMBL_MART_PLANT",
> then I have to use "plants_mart_10", recently it changed back to
> "ENSEMBL_MART_PLANT". I've to mention that both databases contained
> the same species, but the most recent contains also three new.
> It haven't seem that versions of genomes changed.
> 
> HTH,
> Maciej Jończyk
> 
> > I used to access Ensembl 54 database with the biomaRt package. The
> > command
> > below was taken from one of the biomaRt tutorials on the bioconductor
> > website. This commands used to work properly and I was able to query
> > the
> > database but something has recently changed I believe, as this
> > command
> > doesn't work anymore. I have updated my packages and R...  Any clues
> > how
> > can I still query this version? What I want to do is work in hg18
> > coordinates, for this reason I am querying the archived db.
> >
> >
> > ensembl54=useMart("ENSEMBL_MART_ENSEMBL", host="
> may2009.archive.ensembl.org/biomart/martservice/",
> dataset='hsapiens_gene_ensembl')
> >
> > Error in bmAttrFilt("attributes", mart, verbose = verbose) :
>    biomaRt error: looks like we're connecting to incompatible version of
> BioMart suite.
> 
> 
> --
> Maciej Jonczyk,
> Department of Plant Molecular Ecophysiology
> Faculty of Biology, University of Warsaw
> 02-096 Warsaw, Miecznikowa 1
> Poland
> 
> 
> 
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