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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