Hello,

I'm trying to import NCI pathways (available in biopax format) to graphNEL
objects.

This question was already asked on the list but with no fully satisfactory
answer (for my purpose):

- Some pointed to Rredland, which I tried and it indeed seems to parse the
.owl properly, but then the conversion to graphNEL is not straightforward.

- GeneAnswers was also mentioned, but from what I saw in the documentation,
it only loads the gene lists, not the graph of the interactions between the
genes in the pathway.

- Finally, somebody proposed to use the sif format, which would be fine for
a very simplified DAG, but I would need to keep the type of interactions
too.

Has anyone solved the problem since the last thread?

Thanks,

Laurent

-- 
Laurent Jacob
Department of Statistics
UC Berkeley
http://cbio.ensmp.fr/~ljacob

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