Hi Robin and David, Thanks for looking into this issue for me. Please let me know who would be the person to contact for questions about the biomaRt module for R if this is taken care of by someone else.
Thanks, Stan ________________________________ From: Robin Haw [[email protected]] Sent: June 26, 2012 12:47 PM To: Stanley Ng Cc: [email protected]; Francis Ouellette; [email protected]; Arek Kasprzyk Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error Hi Stanley, I might defer to my colleague David Croft for some additional input here. Robin From: Stanley Ng <[email protected]<mailto:[email protected]>> Date: Tuesday, 26 June, 2012 12:42 PM To: Robin Haw <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, Francis Ouellette <[email protected]<mailto:[email protected]>>, David Croft <[email protected]<mailto:[email protected]>>, Arek Kasprzyk <[email protected]<mailto:[email protected]>> Subject: RE: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error Hi Robin, I am using the new email system here at UofT but thanks for forwarding the email to me. I tried using the attribute name "referencedatabase_ncbi_gene" but it gave me the following error message. Please let me know if I need a certain version of biomaRt for my query to work or if there is another name for the attribute (the output of listAttributes(mart) still lists "referencedatabase_entrez_gene" and there is no mention of ncbi anywhere). I am currently using biomaRt_2.10.0 with R version 2.14.2 (2012-02-29). Command and Error: > entrezids = > getBM(attributes=c("referencedatabase_ncbi_gene"),filters="pathway_id_ > list",values=c(pathwayids[1]), mart=mart) Error in getBM(attributes = c("referencedatabase_ncbi_gene"), filters = "pathway_id_list", : Invalid attribute(s): referencedatabase_ncbi_gene Please use the function 'listAttributes' to get valid attribute names Thanks, Stan ________________________________ From: Arek Kasprzyk [[email protected]<mailto:[email protected]>] Sent: June 26, 2012 4:38 AM To: Robin Haw Cc: Stanley Ng; [email protected]<mailto:[email protected]>; Francis Ouellette; [email protected]<mailto:[email protected]> Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error Robin and David: Thank you for clarifying this. It would be great if you could keep such communications on the "users" mailing lists. There are other users who can benefit from this information and if there is an action required with regards to syncing BioPortal with Reactome I can coordinate with Francis so that there are no service disruptions to the user community thank you a On Tue, Jun 26, 2012 at 3:01 AM, Robin Haw <[email protected]<mailto:[email protected]>> wrote: 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]<mailto:[email protected]>] Sent: 25 June 2012 18:23 To: Robin Haw Cc: [email protected]<mailto:[email protected]>; Francis Ouellette; [email protected]<mailto:[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]<mailto:[email protected]>] Sent: June 25, 2012 5:51 PM To: Stanley Ng Cc: [email protected]<mailto:[email protected]>; Francis Ouellette; [email protected]<mailto:[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]<mailto:[email protected]> [[email protected]<mailto:[email protected]>] on behalf of David Croft [[email protected]<mailto:[email protected]>] Sent: 22 June 2012 10:42 To: [email protected]<mailto:[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]<mailto:[email protected]> > https://lists.reactome.org/mailman/listinfo/reactome-help _______________________________________________ Reactome-help mailing list [email protected]<mailto:[email protected]> https://lists.reactome.org/mailman/listinfo/reactome-help ________________________________________ From: Stanley Ng [[email protected]<mailto:[email protected]>] Sent: 25 June 2012 16:50 To: Robin Haw Cc: [email protected]<mailto:[email protected]>; Francis Ouellette; [email protected]<mailto:[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]<mailto:[email protected]> Cc: [email protected]<mailto:[email protected]>; Robin Haw; Francis Ouellette ([email protected]<mailto:[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]<mailto:[email protected]>] Sent: June 25, 2012 2:01 PM To: Stanley Ng Cc: [email protected]<mailto:[email protected]>; Robin Haw; Francis Ouellette ([email protected]<mailto:[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]<mailto:[email protected]>> Sender: [email protected]<mailto:[email protected]> Date: Mon, 25 Jun 2012 13:35:19 To: 'Arek Kasprzyk'<[email protected]<mailto:[email protected]>> Cc: <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query Error _______________________________________________ Users mailing list [email protected]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead www.biomart.org<http://www.biomart.org>
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