[BioC] anybody parsing BioPAX 2?

[Paul Shannon]

Hi Michael,

Thanks for the suggestion.

Last I looked, Rredland was a bit of a chore to install on a Mac; it was enough to deter me.  It appears to need librdf and BerkeleyDB.

Has anyone had any luck with installing it on OSX 10.5 or later?

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 thought....

 - Paul



On May 19, 2010, at 6:37 PM, Michael Lawrence wrote:

> I think that Rredland might help, since BioPAX is RDF. I think the package even has some BioPAX examples.
> 
> Michael
> 
> On Wed, May 19, 2010 at 6:26 PM, Paul Shannon <pshannon at systemsbiology.org> wrote:
> I wish to parse pathways from NCI/Nature Pathway Interaction Database into graphNELs.  They are available as BioPAX, with an '.owl' file extension.
> 
> Has anybody already done this?  I have a start on the task using the XML package, but don't wish to replicate work already done.
> 
> Thanks!
> 
>  - Paul
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