Just want to add that as no host is specified in the biomaRt query, by default, the R package will send the query to the central BioMart repository and will get the list of valid attributes from here:
http://www.biomart.org/biomart/martservice?type=attributes&dataset=pathway&mart=REACTOME which lists: referencedatabase_entrez_gene Gene Entrez ID naive_attributes html,txt,tsv,xls pathway__referencednasequence__dm <http://www.biomart.org/biomart/martservice?type=registry>So it indicates referencedatabase_entrez_gene is a valid attribute but if the user actually uses it and sends the XML query: <?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' requestid= "biomaRt"> <Dataset name = 'pathway'><Attribute name = 'referencedatabase_entrez_gene'/><Filter name = 'pathway_id_list' value = 'test' /></Dataset></Query> To the central repository, the central repository returns the error that says this attribute does not exists....: Query ERROR: caught BioMart::Exception::Usage: Attribute referencedatabase_entrez_gene NOT FOUND</pre> Is the central repository forwarding this query to the actual Reactome BioMart at http://www.reactome.org:5555/biomart/martservice? and might this BioMart be out of sync with the central repository? Steffen On Tue, Jun 26, 2012 at 10:25 AM, Arek Kasprzyk <[email protected]>wrote: > Hi Stan, > I agree with Steffen. The attribute that you are looking for seems to be > missing in the pathway dataset. I just checked on the Reactome Mart site > and only can see the following atts for gene refs: > > <Attribute name = "stableidentifier_identifier" /> > <Attribute name = "referencedatabase_ncbi_gene" /> > <Attribute name = "referencedatabase_ensembl" /> > <Attribute name = "referencedatabase_kegg_gene" /> > <Attribute name = "referencedatabase_omim" /> > <Attribute name = "referencednasequence__dm_db_id" /> > <Attribute name = "referencednasequence__dm__displayname" /> > <Attribute name = > "referencednasequence__dm_species__displayname" /> > > > > Perhaps David would like to comment here? > > > a > > > > On Tue, Jun 26, 2012 at 6:08 PM, Stanley Ng <[email protected] > > wrote: > >> Hi Steffen, >> >> Thanks for your input. >> >> I had originally been querying for the attribute >> "referencedatabase_entrez_gene" and it was working one month ago but I >> tried that query since last week and it gives the below error message so >> I'm not sure if the attribute name may be changed to something else or if I >> need to update to a newer biomaRt package in R? >> >> > 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 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::Usage: Attribute >> referencedatabase_entrez_gene NOT FOUND</pre> >> >> ------------------------------ >> *From:* Steffen Durinck [[email protected]] >> *Sent:* June 26, 2012 12:58 PM >> *To:* Stanley Ng >> *Cc:* Robin Haw; Francis Ouellette; Arek Kasprzyk; [email protected] >> >> *Subject:* Re: [BioMart Users] Stanley Ng - R Biomart Reactome Query >> Error >> >> Hi Stan, Robin, >> >> I'm the biomaRt developer, I've been reading through the email thread >> an am not sure if I understand what the problem is. >> The error is thrown by the biomaRt package as there is no attribute named >> 'referencedatabase_ncbi_gene' in the reactome pathway dataset. I see >> 'referencedatabase_entrez_gene' does exists, and think that is the >> attribute that the user is querying for, that should work. >> >> >> Cheers, >> Steffen >> >> On Tue, Jun 26, 2012 at 9:52 AM, Stanley Ng < >> [email protected]> wrote: >> >>> 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]> >>> Date: Tuesday, 26 June, 2012 12:42 PM >>> To: Robin Haw <[email protected]> >>> Cc: "[email protected]" <[email protected]>, Francis Ouellette < >>> [email protected]>, David Croft <[email protected]>, Arek Kasprzyk < >>> [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]] >>> *Sent:* June 26, 2012 4:38 AM >>> *To:* Robin Haw >>> *Cc:* Stanley Ng; [email protected]; Francis Ouellette; [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]> 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 >>> >>> _______________________________________________ >>> Users mailing list >>> [email protected] >>> https://lists.biomart.org/mailman/listinfo/users >>> >>> >> >> _______________________________________________ >> 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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