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laurent jacob
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100
@laurent-jacob-4466
Last seen 10.3 years ago
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 <http: cbio.ensmp.fr="" %7eljacob="">
--
Laurent Jacob
Department of Statistics
UC Berkeley
http://cbio.ensmp.fr/~ljacob <http: cbio.ensmp.fr="" %7eljacob="">
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