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@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:
>> &lt;?xml version="1.0" encoding="UTF-8"?&gt;
>> &lt;!DOCTYPE Query&gt;
>> &lt;Query  virtualSchemaName = "default" limitStart = "" limitSize  
>> = "200"
>> count = "" softwareVersion = "0.6" requestId= "biomart-client"&gt;
>>        &lt;Dataset name = "uniprot" interface = "default" &gt;
>>                                &lt;Attribute name = "accession" /&gt;
>>                                &lt;Attribute name = "name" /&gt;
>>          &lt;/Dataset&gt;
>> &lt;/Query&gt;
>>
>> 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)
>> ---
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
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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.


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