Data journeys beyond databases in systems biology: Cytoscape and NDEx

Abstract

This chapter investigates how data travels beyond databases in cell biology by focusing on Cytoscape, a platform that has been developed to represent networks, and NDEx, a database that allows for the reuse of network representations. I begin with a brief review of the databases that have been developed for data involving, for example, protein-protein interactions, that are relational and hence productively represented in networks. Given the amount of data stored in modern databases, raw network representations are typically hairballs that provides researchers little useful information other than that lots of things interact. Cytoscape was created by systems biologists to facilitate moving beyond hairballs to informative representations. It provides tools for clustering nodes and annotating them according to what is known about the objects represented. I provide examples of how Cytoscape has been deployed to develop new knowledge about biological mechanisms. Cytoscape has been made freely available, and I describe how a large interational community of researchers has created Apps that enable researchers to make a number of more specialized inferences. NDEx, created by members of the same research lab, serves as an Expo for networks- researchers can share networks they have developed and other researchers can search for networks and made them the basis for further incorporation of data or analyses.