While for several model organisms like Saccharomyces cerevisiae (5) and Caenorhabditis elegans (6), such comprehensive functional interaction networks are available, the larger part of the human interactome remains undiscovered (7). Even worse, the existing knowledge on human functional interactions is dispersed in over 200 interaction databases, each of which has a specific data format, focus and bias (8). Most integration efforts with respect to interaction data so far have focused on merging homogeneous interaction networks. For example, APID (9), MiMI (10) and UniHI (11) integrate protein–protein interaction networks from multiple sources. However, the integration of heterogeneous interactions remains a challenge. Such integration is highly relevant because the resulting network reflects multiple functional aspects of the nodes at the same time (like regulatory relations, physical interactions, catalyzed reactions), and thus constitutes a more complete picture of the living system.
