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))

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_entrez_gene' in 'field list'

</pre>

Can anyone advise on what might be wrong?

Thanks,

Stan