Dear Stanley, Is this still a problem? I thought we'd been able to address this issue, last week?
If not, can you please let us know? Thanks, Robin ________________________________________ From: [email protected] [[email protected]] on behalf of David Croft [[email protected]] Sent: 22 June 2012 10:42 To: [email protected] Subject: Re: [Reactome-help] [Contact-us] Biomart query from R no longer working? Hi Stanley, Sorry about this problem, we got caught out by a database name change: Entrez gene is now NCBI gene. We have now updated our BioMart to reflect this, so if you run the query on our website, it should work. I do not have any experience with R-BioMart, you may need to experiment a little. Cheers, David Croft. > I am a PhD student working on leukemia at the university of toronto. > > About a month ago, I ran the following query which returned a list of entrez > gene ids for the pathways that I was interested in. > > "library("biomaRt"); > > mart = useMart("REACTOME", dataset="pathway") > > pathwayids = > getBM(attributes=c("stableidentifier_identifier"),filters="species_selection",values=c("Homo > sapiens"), mart=mart) > > entrezids = > getBM(attributes=c("referencedatabase_entrez_gene"),filters="pathway_id_list",values=c(pathwayids[i]), > mart=mart)" > > However I tried to run that same query today through R biomart and it no > longer works. I see the following error and was wondering if the query > requirements have changed for what I am seeking? > > " > Error in getBM(attributes = c("referencedatabase_entrez_gene"), filters = > "pathway_id_list", : > Query ERROR: caught BioMart::Exception::Query: 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' > > " > _______________________________________________ > Reactome-help mailing list > [email protected] > https://lists.reactome.org/mailman/listinfo/reactome-help _______________________________________________ Reactome-help mailing list [email protected] https://lists.reactome.org/mailman/listinfo/reactome-help ________________________________________ From: Stanley Ng [[email protected]] Sent: 25 June 2012 16:50 To: Robin Haw Cc: [email protected]; Francis Ouellette; [email protected] Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error Hi Robin, When do you think this can be fixed? Thanks, Stan ________________________________________ From: Stanley Ng Sent: June 25, 2012 3:41 PM To: [email protected] Cc: [email protected]; Robin Haw; Francis Ouellette ([email protected]) Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error Hi Arek, Thanks for clarifying. I had thought it may have been a new issue. Stan ________________________________________ From: arek kasprzyk [[email protected]] Sent: June 25, 2012 2:01 PM To: Stanley Ng Cc: [email protected]; Robin Haw; Francis Ouellette ([email protected]) Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error Hi Stan This is still the same problem. Hopefully Robin Haw (cc'ed on this emai)l will be able to help you Sent from my BlackBerry® smartphone on O2 -----Original Message----- From: Stanley Wai-Kwong Ng <[email protected]> Sender: [email protected] Date: Mon, 25 Jun 2012 13:35:19 To: 'Arek Kasprzyk'<[email protected]> Cc: <[email protected]> Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
