[ensembl-dev] biomaRt troubles

[Julien Roux]

Dear Thomas,

You're right it works now!

library(biomaRt)
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", 
dataset="drerio_gene_ensembl", host="jul2016.archive.ensembl.org")

Thanks!
Julien

On 8/31/16 10:59 AM, Thomas Maurel wrote:
> Dear Julien,
>
> Our ensembl gene mart via the R package seems to be working fine for 
> me this morning:
>
> > mart <- 
> useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="www.ensembl.org 
> <http://www.ensembl.org>")
> > 
> getBM(attributes=c('ensembl_gene_id','ensembl_transcript_id','description'),filters 
> = 'ensembl_gene_id', values = 'ENSG00000252303', mart = mart)
>   ensembl_gene_id ensembl_transcript_id description
> 1 ENSG00000252303       ENST00000516494 RNA, U6 small nuclear 280, 
> pseudogene [Source:HGNC Symbol;Acc:HGNC:47243]
>
> Could you please let me know:
>
>     1) The mart that you are using
>     2) The ensembl website that you are pointing to
>     3) The error that you are getting
>
>
> Thanks a lot,
> Regards,
> Thomas
>> On 31 Aug 2016, at 07:51, Julien Roux <julien.roux at unil.ch 
>> <mailto:julien.roux at unil.ch>> wrote:
>>
>> Dear Ensembl team,
>>
>> Thanks for bringing the website up, it was missed a lot! ;)
>>
>> This morning I have trouble to connect to the database via the R 
>> package BiomaRt (the web version of biomart works just fine). Is this 
>> related to the downtime?
>>
>> Best,
>>
>> Julien
>>
>> -- 
>> Julien Roux
>> Department of Ecology and Evolution, University of Lausanne, Switzerland
>> http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html
>> Tel: +41 78 700 2931
>> Twitter: @_julien_roux
>>
>>
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>
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
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-- 
Julien Roux
Department of Ecology and Evolution, University of Lausanne, Switzerland
http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html
Tel: +41 78 700 2931
Twitter: @_julien_roux

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