[BioC] Fwd: Connecting to Uniprot Biomart using biomaRt

[Dan Tenenbaum]

---------- Forwarded message ----------
From: Rhoda Kinsella <rhoda at ebi.ac.uk>
Date: Tue, Oct 25, 2011 at 3:20 AM
Subject: Re: [BioC] Connecting to Uniprot Biomart using biomaRt
To: Rhoda Kinsella <rhoda at ebi.ac.uk>
Cc: Dan Tenenbaum <dtenenba at fhcrc.org>, kenny daily
<kmdaily at gmail.com>, bioconductor at r-project.org


HI Dan and Kenny,
I have received a message from the UniProt team to say that the
UniProt mart is now back up and running.
Regards
Rhoda
On 25 Oct 2011, at 08:55, Rhoda Kinsella wrote:

Hi Dan and Kenny
The message I sent about downtime related to the Ensembl marts only as
this is what I maintain at the EBI. I have taken a look at the UniProt
mart at the EBI and there seems to be a problem with it. I will
contact the UniProt team and let them know there is an issue.
Thank you for reporting this,
Regards
Rhoda



On 24 Oct 2011, at 18:39, Dan Tenenbaum wrote:

Hi Kenny,

On Mon, Oct 24, 2011 at 9:49 AM, kenny daily <kmdaily at gmail.com> wrote:

Hi,

I'm unable to use the Uniprot Biomart. Are there new settings to connect to

this mart? Thanks!

require(biomaRt)

uniprotV <- useMart("unimart", dataset="uniprot")

d <- getBM(attributes=c("accession", "name"), mart = uniprotV)

Error in getBM(attributes = c("accession", "name"), mart = uniprotV) :

 Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred

at web service based data source!

Remote data source: http://www.ebi.ac.uk:80/uniprot/biomart/martservice?

Query XML:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE Query>

<Query  virtualSchemaName = "default" limitStart = "" limitSize = "200"

count = "" softwareVersion = "0.6" requestId= "biomart-client">

       <Dataset name = "uniprot" interface = "default" >

                               <Attribute name = "accession" />

                               <Attribute name = "name" />

         </Dataset>

</Query>

Please ensure the above query XML is well-formed and does not contain

illegal characters.

Error message from remote server as below:

Query ERROR: caught BioMart::Exception::Usage: WITHIN Virtual Schema :

default, Dataset uniprot NOT FOUND</pre>



This could be related to the scheduled downtime of the Biomart
servers, which was supposed to end by noon UK time today (Monday). The
announcement is here:

https://stat.ethz.ch/pipermail/bioconductor/2011-October/041685.html

I've sent a note to Rhoda asking about the server status. Will pass
along what I find out.

Dan


--

Kenny Daily

http://www.kennydaily.net/

--- Prediction is very difficult, especially about the future. (Niels Bohr)

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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.