I would like to construct a mathematical graph: $G = (E,V, w(E))$ a graph with vertices, edges with weight on them based on a KEGG pathway.
Is there a way to do that with existing tools? If not I will start to implement a Python module for that. My main question is what is the mathematical graph representation of pathways? Assuming the possible node types and the different connections?
I would like to transform a pathway to a graph because then one can run min-cut-max-flow algorithms and stuff like that as part of my pathway analysis.