Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.
HyBrow: a prototype system for computer-aided hypothesis evaluation
The Huck Institute for Life Sciences, Penn State University, University park, PA 16801, USA
Received on January 15, 2004; accepted on March 1, 2004
Motivation: Experimental design, hypothesis-testing and model-building in the current data-rich environment require the biologists' to collect, evaluate and integrate large amounts of information of many disparate kinds. Developing a unified framework for the representation and conceptual integration of biological data and processes 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.
Results: We have developed the HyBrow (Hypothesis Browser) system as a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. HyBrow consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology and programs to perform hypothesis design and evaluation. We demonstrate the HyBrow prototype using the galactose gene network in Saccharomyces cerevisiae as our test system, and evaluate alternative hypotheses for consistency with stored information.
Availability: www.hybrow.org
Contact: nigam{at}psu.edu
* To whom correspondence should be addressed.
The authors wish to be known that, in their opinion, the first two authors should be regarded as joint first authors.
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