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The purpose of this work is to outline the first steps taken towards the building of an automatic interpretation and hypothesis generation machine. The contents of this thesis describe the framework built to parse and manipulate the knowl- edge assemblies encoded in BEL, which enables BEL to act as a semantic inte- gration layer for heterogeneous data and knowledge sources, the development of a framework for automatic integration of relevant knowledge from structured sources, and the development of schema-free analytical techniques to generate data-driven hypothesis.