One of the main challenges for the development of spatial information theory is the formalization of the concepts of space and spatial relations. Currently, most spatial data structures and spatial analytical methods used in GIS embody the notion of space as a set of absolute locations in a Cartesian coordinate system, thus failing to incorporate spatial relations, which are dependent on topological connections and fluxes between physical or virtual networks. To answer this challenge, we introduce the idea of a generalized proximity matrix (GPM), an extension of the spatial weights matrix where the weights are computed taking into account both absolute space relations such as Euclidean distance or adjacency and relative space relations such as network connection. Using the GPM, two geographic objects (e.g. municipalities) are "near" each other if they are connected through a transportation or telecommunication network, even if thousands of kilometers apart or, using even trac...