[BioC] how to store multiple relationships between nodes in graphNEL?

Paul Shannon pshannon at systemsbiology.org
Tue Jul 24 20:53:58 CEST 2007

I'd like to find the best way to record multiple relationships  
between nodes
in a graphNEL object.  The data for my graph comes from DIP, the  
Database of
Interacting Proteins, where many protein interactions have several  
kinds of evidence.
In other settings, I represent this as multiple edges, another solution
is needed here, since graphNEL is designed for at most one edge  
between nodes.

So I am  improvising, packing any number of experimental methods into  
a token-separated
list in a single edge's edgeData.  Here is an example of  one pair of  
yeast proteins observed
by three different methods:

   edgeData (g, 'YCR084C', 'YBR112C', attr='edgeType')
      [1] "Immunoprecipitation::Affinity chromatography::Gel  
filtration chromatography"

Could I be doing this a better way?  And how could I best store the
pubmed id associated with each method?

Thank you,

  - Paul

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