Hi Arek,
Thanks for looking into this for me. Regards, Stan From: Arek Kasprzyk [mailto:[email protected]] Sent: June-21-12 10:44 AM To: Stanley Wai-Kwong Ng Cc: [email protected]; Robin Haw Subject: Re: Stanley Ng - R Biomart Reactome Query Error Hi Stan, this looks like misconfiguration on the Reactome side. I am forwarding your email to the Reactome mart administrators who will be able to help with that a On Thu, Jun 21, 2012 at 3:08 PM, Stanley Wai-Kwong Ng <[email protected]> wrote: Hi Arek, I am a PhD student at the University of Toronto and am using biomart in R to get a list of entrez gene Ids for some reactome pathways in humans. I ran the following query last month and it worked with no problems: library("biomaRt") mart = useMart("REACTOME", dataset="pathway") pathwayids = getBM(attributes=c("stableidentifier_identifier"),filters="species_selection ",values=c("Homo sapiens"), mart=mart) pathwayids = c(do.call("cbind",pathwayids)) entrezids = getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list ",values=c(pathwayids[i]), mart=mart) However, I tried to run the commands again last night and today and I get the following error: Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = "pathway_id_list", : Query ERROR: caught BioMart::Exception::Query: <pre>Query error occurred at web service based data source! Remote data source: http://www.reactome.org:5555/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 = "pathway" interface = "default" > <Attribute name = "referencedatabase_entrez_gene" /> <ValueFilter name = "pathway_id_list" value = "REACT_1698"/> </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::Database: Error during query execution: Unknown column 'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entr ez_gene' in 'field list' </pre> Can you advise on what might be wrong? Thanks, Stan -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead www.biomart.org
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