HyQue is a tool for evaluating scientific hypotheses about molecular events. It has been applied to the domain of the galactose gene network in Saccharomyces cerevisae. Hypotheses are evaluated using the GAL HyQue Knowledge Base (HKB), which contains data about 7 types of events: protein-protein binding, protein-nucleic acid binding (including binding to gene promoters), transcription activation and inhibition, inducing gene expression, repressing gene expression and the transport of chemicals within parts of cells. HyQue features a flexible knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated according to experimental and literature-sourced evidence using SPARQL Inferencing Notation (SPIN) rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis.