[ensembl-dev] biomaRt issue

Thomas Maurel maurel at ebi.ac.uk
Wed Apr 15 15:48:01 BST 2015

Dear Julien,

Yes, this is the right place to post this since you are querying the Ensembl marts on ensembl.org ;-)
There is nothing wrong with your code, I’ve just tried your query and got the result in few minutes:
> library("biomaRt")
> ensembl71 <- useMart(host='apr2013.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl')
> GO <- getBM(attributes=c(‘go_id', 'name_1006', 'namespace_1003'), mart = ensembl71)
> head(GO)
       go_id                                    name_1006     namespace_1003
1 GO:0007186 G-protein coupled receptor signaling pathway biological_process
2 GO:0016021                         integral to membrane cellular_component
3 GO:0005886                              plasma membrane cellular_component
4 GO:0004930          G-protein coupled receptor activity molecular_function
5 GO:0004984                  olfactory receptor activity molecular_function
6 GO:0008150                           biological_process biological_process

It could be that our website our your internet connection had a glitch. Could you please try again?
You could also try to update the BiomaRt package to the current 2.20 version (http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html <http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html>) and update your R software version.
It’s also good practice to refrain yourself from running full genome queries with BioMart, an easy way around this is to us filters to break down your query in smaller pieces (e.g: to filter on chromosome names).

Hope this helps,
> On 15 Apr 2015, at 15:34, Julien Roux <julien.roux at unil.ch> wrote:
> Hi all,
> Not sure this is the right place to post this, please redirect me if not.
> I'm having troubles retrieving data with biomaRt (2.18) from Ensembl 71
> > library("biomaRt")
> > ensembl71 <- useMart(host='apr2013.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl')
> > GO <- getBM(attributes=c('go_id', 'name_1006', 'namespace_1003'), mart = ensembl71)
> Error in value[[3L]](cond) :
>  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.
> However the fwollowing commands work well, so I wonder if the service is really down or if there is some other issue
> > listFilters(ensembl71)
> > listAttributes(ensembl71)
> Best
> Julien
> -- 
> Julien Roux
> Marie-Curie postdoctoral fellow
> 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
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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

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