cannot connect to REACTOME database in R
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Entering edit mode
jz6002 • 0
@jz6002-6980
Last seen 6.3 years ago
Canada

I tired to access the REACTOME database by the following R code which I always did as following:

library("biomaRt")
reactome=useMart("REACTOME")
pathway=useDataset("pathway",mart=reactome)
I got the error MSG as following:
Error in useDataset("pathway", mart = reactome) : 
  The given dataset:  pathway , is not valid.  Correct dataset names can be obtained with the listDatasets function.
Then I used listDatasets(reactome) to see all the datasets under REACTOME. I got no datasets under it.
[1] dataset description version
 <0 rows> (or 0-length row.names)
Is the REACTOME database down or there is some problem with the connection?

It used to work for me. But I tried last Friday, it didn't work till now.

biomart REACTOME • 954 views
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Entering edit mode
@steffen-durinck-4894
Last seen 7.3 years ago

Hi,

The Reactome BioMart instance is not being maintained and therefore unfortunately currently not available.

Hopefully it will come back online at a future date.

Cheers,

Steffen

 

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