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
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