Is there anyway to get BioGrid gene interaction network automatically using R?

Question

[Na Sed]

Is there anyway to get BioGrid gene interaction network automatically using R?

Answer 1

[Rajarshi Guha]

Coincidence! I've just been putting together an R client for BioGRID. Very rough initial version is at https://github.com/rajarshi/cdkr/tree/master/rbiogrid. To install

library(devtools)
install_github("cdkr", "rajarshi", subdir="rbiogrid")

You will need to get an access key from the BioGRID website. Right now it has no tests and has basic functionality to get interactions by gene names. It sets a number of arguments by default (e.g., selfInteractionsExcluded = TRUE, includeInteractorInteractions = FALSE) - you can view the source of the function to see them.

Example usage is

library(rbiogrid)
set.access.key('XXXX')
get.interactions('PLK1')

[Na Sed]

Thank you.

When I am trying to run the code, I get this error:

Error in function (type, msg, asError = TRUE)  :
  Failed to connect to webservice.thebiogrid.org port 80: Timed out

Do you know why this happens?

[Rajarshi Guha]

Not sure. The code works fine from here. Does http://webservice.thebiogrid.org/ resolve properly?

Answer 2

[Pierre Lindenbaum]

yes, use the REST service http://wiki.thebiogrid.org/doku.php/biogridrest and the R methods to access the web http://www.math.ucla.edu/~anderson/rw1001/library/base/html/read.table.url.html