Hi All,
I tried using biomart in R again today and got a different error than
before.
When trying to return a list of ENTREZ GENE IDs for some REACTOME pathways ,
either the attribute name for entrez gene ids have changed or is missing as
per the below error.
Any advice is appreciated.
Thanks,
Stan
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: Arek Kasprzyk [mailto:[email protected]]
Sent: June-21-12 10:44 AM
To: Stanley Wai-Kwong Ng
Cc: [email protected]; Robin Haw
Subject: Re: Stanley Ng - R Biomart Reactome Query Error
Hi Stan,
this looks like misconfiguration on the Reactome side. I am forwarding your
email to the Reactome mart administrators who will be able to help with that
a
On Thu, Jun 21, 2012 at 3:08 PM, Stanley Wai-Kwong Ng
<[email protected]> wrote:
Hi Arek,
I am a PhD student at the University of Toronto and am using biomart in R to
get a list of entrez gene Ids for some reactome pathways in humans.
I ran the following query last month and it worked with no problems:
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[i]), mart=mart)
However, I tried to run the commands again last night and today and I get
the following error:
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::Database: Error during query
execution: Unknown column
'test_reactome_mart.pathway__referencednasequence__dm.referencedatabase_entr
ez_gene' in 'field list'
</pre>
Can you advise on what might be wrong?
Thanks,
Stan
--
Arek Kasprzyk, MD, MSc, PhD
BioMart Project Lead
www.biomart.org
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