  Pathways are integral to systems biology. Their classical representation has
proven useful but is inconsistent in the meaning assigned to each arrow (or
edge) and inadvertently implies the isolation of one pathway from another.
Conversely, modern high-throughput experiments give rise to standardized
networks facilitating topological calculations. Combining these perspectives,
we can embed classical pathways within large-scale networks and thus
demonstrate the crosstalk between them. As more diverse types of
high-throughput data become available, we can effectively merge both
perspectives, embedding pathways simultaneously in multiple networks. However,
the original problem still remains - the current edge representation is
inadequate to accurately convey all the information in pathways. Therefore, we
suggest that a standardized, well-defined, edge ontology is necessary and
propose a prototype here, as a starting point for reaching this goal.
