[ensembl-dev] biomaRt issue

[Julien Roux]

Thanks Thomas,
Indeed the problem was with the internet connection, I'll be careful 
next time I connect from a coffee shop wiki spot ;)
Best,
Julien

On 4/15/15 4:48 PM, Thomas Maurel wrote:
> Dear Julien,
>
> Yes, this is the right place to post this since you are querying the 
> Ensembl marts on ensembl.org <http://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
>     <http://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) 
> 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,
> Regards,
> Thomas
>> On 15 Apr 2015, at 15:34, Julien Roux <julien.roux at unil.ch 
>> <mailto: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 
>> <http://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
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
>
>
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-- 
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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