Hi Marko, this looks to me like a configuration problem on the Uniprot side. I have cc'ed Steven who would be able to confirm that this problem is rectified in the latest Uniprot release (BioPortal we'll be upgrading to the lates Uniprot soon)
a On Fri, Mar 2, 2012 at 2:20 AM, Marko Laakso <[email protected]>wrote: > Dear BioMart user, > > I have faced some issued in querying Ensembl IDs and EC numbers from > UniProt. > > The following Bio Portal bookmark demonstrates this issue: > > http://central.biomart.org/**martwizard/#!/Protein_** > sequence_and_structure?mart=**UniProt+(EBI%2C+UK)&step=4&** > proteome_name=Homo+sapiens&**attributes=ensembl_id%2Cec_**number<http://central.biomart.org/martwizard/#!/Protein_sequence_and_structure?mart=UniProt+(EBI%2C+UK)&step=4&proteome_name=Homo+sapiens&attributes=ensembl_id%2Cec_number> > > The WWW interface does not tell anything about the actual causes. However, > the same query fails when I am accessing Biomart from the > Bioconductor in R (biomaRt package). The query is sent to: > http://www.ebi.ac.uk:80/**uniprot/biomart/martservice<http://www.ebi.ac.uk:80/uniprot/biomart/martservice> > ? > > The exact query XML looks like this: > > <?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 = "ensembl_id" /> > <Attribute name = "ec_number" /> > <ValueFilter name = "proteome_name" value = "Homo sapiens"/> > </Dataset> > </Query> > > Now, the error message is: > > Error message from remote server as below: > Query ERROR: caught BioMart::Exception::Database: Error during query > execution: Table 'unimart.uniprot__db2ensembl__**dm' doesn't exist > > Best regards, > Marko Laakso > ______________________________**_________________ > Users mailing list > [email protected] > https://lists.biomart.org/**mailman/listinfo/users<https://lists.biomart.org/mailman/listinfo/users> > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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