HyBrow: A Hypothesis Space Browser
Nigam Shah1, Stephen Racunas2, Nina V. Fedoroff
1nigam@psu.edu, Penn State University; 2sar147@psu.edu, Penn State University
Representation of diverse data and biological processes in a single formalism is a major challenge in bioinformatics because of the variety of available data and the different levels of detail at which biological processes can be considered. We have developed an event-based ontology for representing both biological processes and data from different sources at varying levels of detail. We have integrated this ontology with a discrete event systems framework to support qualitative reasoning. The framework adopts a hierarchical, contradiction-based approach to evaluate competing hypotheses based on available data and provide a ranking among them. We have designed a database backend to structure information in the ontology and programs to perform contradiction-based evaluation of hypotheses constructed using the ontology. We have also designed command line, web and custom interfaces for the system. We have named our system Hybrow (from Hypothesis Browser), which includes the event-based ontology, an associated database, the hypothesis evaluation framework and the interface programs. We demonstrate the feasibility of HyBrow, using the galactose metabolism gene network in Saccharomyces cerevisiae as our test system, for ranking alternative hypotheses in an automated manner using available data.