On Wed, May 19, 2010 at 9:50 PM, Paul Shannon
<pshannon@systemsbiology.org>wrote:

> 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.
>

redland now has SQLite back end capabilities, and I have been trying to find
time to replace the berkeley db interface with interface SQLite.  i will try
to do it in the next few weeks.


>
> 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@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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> >
>
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