[BioC] anybody parsing BioPAX 2?

Emek Demir demir at cbio.mskcc.org
Wed Jun 9 23:35:25 CEST 2010

Paul Shannon <pshannon at ...> writes:
> Actually, parsing the owl/BioPAX xml is not -so- hard using the XML package. 
But there are quite a few ways
> the data could be mapped to a graphNEL.  I wonder if anyone has given this any

Hi Paul,

You can do several things - I would give paxtools a try, you can use an
R-to-Java bridge like rJava. 

Alternatively you can use the sif format used provided by pathway commons
(www.pathwaycommons.org) as it already provides an easier to handle, reduced
graph, with some of the conversions you mentioned. Conversion is lossy - but
maybe this is the right level of detail for your purpose, I don't know.


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