HyQue: Evaluating hypotheses using Semantic Web technologies

TitleHyQue: Evaluating hypotheses using Semantic Web technologies
Publication TypeConference Paper
Year of Publication2010
AuthorsCallahan, A, Dumontier, M, Shah, NH
Conference NameBio-ontologies 2010: Semantic Applications in Life Sciences
Date Published2010
Conference LocationBoston, USA
KeywordsBioinformatics, Ontology, Semantic Web
AbstractKey to the success of e-Science is the ability to evaluate complex knowledge and expert-composed hypotheses by checking their validity against supporting experimental data. Motivated by the HyBrow Hypothesis Browser, we present HyQue, a Semantic Web-based tool for querying and evaluating scientific hypotheses. HyQue features a flexible knowledge model to accommodate diverse hypotheses structured as events and represented using Se-mantic Web languages (RDF/OWL). Hypothesis validity is evaluated according to experimental and literature-sourced evidence through a unique combination of SPARQL queries and query evaluation 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. Unlike HyBrow, this system is capable of executing queries where participating entities or event types are unspecified, thus opening the door to a significantly wider range of hypothesis support. We use HyQue to evaluate hypotheses with varying levels of detail in the context of the galactose gene network in Saccharo-myces cerevisiae, and demonstrate its feasibility over a growing body of knowledge."