Hi Stan, I'm glad I was able to forward the email to you. I think it should be "referencedatabase_ncbi_gene" instead "referencedatabase_entrez_gene".
Are you using the new utoronto email system? There's some odd behaviour with the sending and receiving some emails with the utoronto mail system. So, this might explain why you did not receive the email earlier because it was definitely sent by our mail server and received at a number of different locations. If you have any other questions, please let me know. Robin ________________________________________ From: Stanley Ng [[email protected]] Sent: 25 June 2012 18:23 To: Robin Haw Cc: [email protected]; Francis Ouellette; [email protected] Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error Hi Robin, Thanks for your email. I didn't receive the below email from David Croft for some reason. (nothing in my inbox or junkmail folders) I have written some small R scripts to help me collect entrez gene IDs for each specified pathway. Do you know what is the new attribute name I should be using to get lists of NCBI gene IDs for pathways through the Biomart R module? i.e., right now i am querying for "referencedatabase_entrez_gene" but it doesn't work anymore, maybe it is called something else now? Commands: 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[1]), mart=mart) Error: Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre> Thanks, Stan ________________________________________ From: Robin Haw [[email protected]] Sent: June 25, 2012 5:51 PM To: Stanley Ng Cc: [email protected]; Francis Ouellette; [email protected] Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error 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
