Hello, coming from the Network Reconstruction Methodology I also ran into the problem of getting BioPAX data into R. I wrote an R package, rBiopaxParser, that allows you to parse the .owl Biopax export from filesystem into R using the XML package. Internally you can access, modify, merge and do some other stuff and if it's still valid BioPAX it can be exported into .owl again. There are alot of convenience function available, see the manual for a complete list. The internal data representation is in a tabular format, quite close to the actual XML/RDF data. Regulatory pathways can be transformed (although this is subject to loss of information, given that only controls are used for these regulatory graphs) into graphs, and can be visualized with Rgraphviz. Parsing is currently restricted to Biopax Level 2, but Im working on integrating Level 3 already. There is quite some documentation (and a walkthrough for the NCI Biocarta data export) in the vignette and the manual. You can find the package at https://github.com/frankkramer/rBiopaxParser direct link to the vignette is: https://github.com/frankkramer/rBiopaxParser/blob/master/inst/doc/rBio paxParserVignette_short.pdf?raw=true If this would be of interest to more users I can probably polish the package some more and try to submit it to bioconductor. Let me know if you encounter any problems or have ideas for new features! Best wishes, Frank -- Frank Kramer University Medical Center G?ttingen Department for Medical Statistics Statistical Bioinformatics http://www.ams.med.uni-goettingen.de/amsneu/kramer-en.html