cannot connect to REACTOME database in R
1
0
Entering edit mode
jz6002 • 0
@jz6002-6980
Last seen 9.3 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 • 1.6k views
ADD COMMENT
0
Entering edit mode
@steffen-durinck-4894
Last seen 10.2 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

 

ADD COMMENT

Login before adding your answer.

Traffic: 863 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6