[Bioperl-l] parsing KGML files
cjfields at illinois.edu
Wed May 27 11:06:54 EDT 2009
Unless something changed, KGML itself is not XML but HTML-like. I
think there are XML conversions for some KGML files at KEGG.
Unfortunately we don't have the facility within bioperl to parse KGML,
but I have used HTML::Parser for KGML in the (distant) past with some
On May 27, 2009, at 12:27 AM, anupam sinha wrote:
> Dear all,
> I am working on evolutionary dynamics of protein
> networks for which I need enzyme-centric metabolic networks(i.e
> nodes in
> this network consists of enzymes and they are connected if the
> product of
> one is a substrate of other and/or they share a common metabolite).
> How can
> I parse KGML (KEGG XML) files to extract information in above
> For example....
> Source_node Destination node
> enzyme1 enzyme2
> enzyme3 enzyme5
> enzyme6 enzyme8
> enzyme1 interacts with enzyme2 because the product of the reaction
> by enzyme1 happens to be the substrate for enzyme2 etc.
> Any help will be appreciated.
> Thanks and Regards,
> Anupam Sinha,
> Graduate Student,
> Centre for DNA Fingerprinting and Diagnostics,
> Hyderabad, India-500001
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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