[ensembl-dev] biomaRt troubles

Thomas Maurel maurel at ebi.ac.uk
Wed Aug 31 09:59:09 BST 2016


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")
> 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> 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

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