Question: cannot connect to REACTOME database in R
0
gravatar for jz6002
5.0 years ago by
jz60020
Canada
jz60020 wrote:

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 • 791 views
ADD COMMENTlink modified 4.9 years ago by Steffen Durinck90 • written 5.0 years ago by jz60020
Answer: cannot connect to REACTOME database in R
0
gravatar for Steffen Durinck
4.9 years ago by
Steffen Durinck90 wrote:

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 COMMENTlink written 4.9 years ago by Steffen Durinck90
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