[BioC] Connecting to Uniprot Biomart using biomaRt

[Dan Tenenbaum]

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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