1. A software implemented method for hypothesizing a biological relationship in a biological system, the method comprising: (a) providing a database of biological assertions comprising a multiplicity of nodes representative of biological elements, relationship descriptors describing relationships between nodes, and characterizing properties of said nodes and relationships; (b) selecting a target node in the database known from experimental observation to correspond to a biological element which increases in number or concentration, decreases in number or concentration, appears within, or disappears from a real biological system when it is perturbed; and (c) performing a backward logical simulation within said database from said target node through said relationship descriptors upstream along a path defined by potentially causative nodes to discern a node hypothetically responsible for the experimentally observed change in said target node.