HyQue hypotheses consist of one or more events in which the participating entities (and, optionally, the physical location and genetic perturbation context) are specified. The HyQue hypothesis ontology defines a hypothesis as some thing that has component part some proposition that specifies some event. Complex hypotheses can be specified by logically combining events and propositions using AND and OR operators, potentially leading to nested event sets e.g. A AND (B OR C). The AND operator indicates that multiple events must be satisfied for the hypothesis to be satisfied. In contrast, the OR operator simply indicates that if any of the specified events have experimental support, they will satisfy the hypothesis. This may be appropriate when multiple mechanisms are possible, such as a phenotype resulting from the activation of more than one pathway. The schematic diagram below shows how hypotheses are related to propositions, events, event data and evaluations. HyQue automatically links hypothesis evaluations to the source hypothesis, as well as the rules used to generate the evaluation.