[ensembl-dev] biomaRt issue
maurel at ebi.ac.uk
Wed Apr 15 15:48:01 BST 2015
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:
> 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)
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)
> Julien Roux
> Marie-Curie postdoctoral fellow
> Department of Ecology and Evolution, University of Lausanne, Switzerland
> Tel: +41 78 700 2931
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Dev