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_entrez_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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