[BioMart Users] General query

[Stanley Wai-Kwong Ng]

Hi All,

 

I 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[1]), 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:

&lt;?xml version="1.0" encoding="UTF-8"?&gt;

&lt;!DOCTYPE Query&gt;

&lt;Query  virtualSchemaName = "default" limitStart = "" limitSize = "200"
count = "" softwareVersion = "0.6" requestId= "biomart-client"&gt;

        &lt;Dataset name = "pathway" interface = "default" &gt;

                                &lt;Attribute name =
"referencedatabase_entrez_gene" /&gt;

                &lt;ValueFilter name = "pathway_id_list" value =
"REACT_1698"/&gt;

          &lt;/Dataset&gt;

&lt;/Query&gt;

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 anyone advise on what might be wrong?

 

Thanks,

Stan

 


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