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
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?
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
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