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]> 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]] > 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 > > > > > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead www.biomart.org
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