---------- Forwarded message ---------- From: Rhoda Kinsella <rhoda@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:

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

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]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor 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.