[Bioperl-l] protein networks

Richard Adams radams at staffmail.ed.ac.uk
Fri Mar 12 16:22:44 EST 2004

Hi Boris,
Thanks for the tips.
I've put some modules in CVS in Bio::Graph namespace.
The module representing a protein interaction network is called 
ProteinGraph.pm, but you're right, including the word "interaction" 
would clarify it. 

The base class, Nat Goodman's SimpleGraph is totally generic  for any
graph, not just biological graphs. ProteinGraph.pm uses Bio::Seq objects
to represent the nodes and only subclasses a few methods from SimpleGraph. 
I would imagine that a protein::DNA and DNA/DNA interactions could also be 
using this class, using the alphabet() method to distinguish proteins from DNA.
If you think that additional data fields /methods would be needed I'd love to 
know - methods in common between the classes could then be abstracted into 
a common Bio::Graph::Base class.

I've include a basic XML parser for parsing PSI XML records. 
my $io = Bio::Graph::IO->new(-file => 'myfile', -format =>'psixml');
my $gr = $io->next_network();
At present it
reads the minimun infor to construct a graph but does not make an effort to
get all the data. If you know of the existence of an industrial strength
PSI-XML parser, I'd be really pleased, there must be one out there somewhere.


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