[Bioperl-l] parsing KGML files

Chris Fields 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  
> interaction
> 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  
> mentioned
> format????
> For example....
> Source_node       Destination node
> enzyme1             enzyme2
> enzyme3             enzyme5
> enzyme6             enzyme8
> enzyme1 interacts with enzyme2 because the product of the reaction  
> catalysed
> 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
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