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frankkramer-lab / rBiopaxParser

Parses BioPAX files (BioPAX Version 2 and BioPAX Version 3 are supported) and represents them in R. There is quite alot of documentation available for this package. See the reference manual and the vignette for examples! If you have any questions or suggestions... DONT BE SHY! Mail me! See package description for an email address.
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Error in function (type, ms, asError=TRUE) Server denied you to change to the given directory #9

Open jordlang01 opened 1 year ago

jordlang01 commented 1 year ago

Hello,

I recently installed and loaded the rBiopaxParser package. However when I ran

file = downloadBiopaxData("NCI")

I received the error "Trying to download: NCI-Nature_Curated.bp2.owl.gz Error in function (type, msg, asError = TRUE) : Server denied you to change to the given directory"

Please advise. Thanks

frankkramer commented 1 year ago

Dear @jordlang01 ,

thanks for the report! Apparently the FTP-Servers were finally shut down.

I found the following information at the NCI: The NCI PID data portal has been retired. PID data are now available for the research community via the [NDEx](http://www.ndexbio.org/) database, hosted by the Ideker Lab at the UC San Diego School of Medicine. To access PID files click “start now” and on the public server welcome page type nci in the search box. NDEx will return all the PID network files. PID data is also available for download in BioPax format on [GitHub](https://github.com/NCIP/pathway-interaction-database/tree/master/download).

Please note, the BioPAX-Level 2 data is not hosted on the GitHub page.

I will update the package as time or workforce becomes availabe.

Best wishes Frank

jordlang01 commented 1 year ago

Dear @frankkramer,

Thanks for letting me know!

Best, Jordan