Access to archived versions of Ensembl with biomaRt

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Adrián Cortés ▴ 10

@adrian-cortes-5039

Last seen 10.5 years ago

Hello, 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. Thanks, Adrian 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. > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] biomaRt_2.10.0 lodplot_1.1 loaded via a namespace (and not attached): [1] RCurl_1.7-0 XML_3.4-3 [[alternative HTML version deleted]]

biomaRt biomaRt • 3.1k views

ADD COMMENT • link updated 13.2 years ago by boczniak767 ▴ 740 • written 13.2 years ago by Adrián Cortés ▴ 10

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boczniak767 ▴ 740

@maciej-jonczyk-3945

Last seen 4 months ago

Poland

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 Jo?czyk > 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 -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com

ADD COMMENT • link 13.2 years ago boczniak767 ▴ 740

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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 Jo?czyk > > > 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 > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 13.2 years ago Malcolm Cook ★ 1.6k

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