title: HyBrow: a prototype system for computer-aided hypothesis evaluation.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  www.hybrow.org
authors.affiliation: The Huck Institute for Life Sciences, Penn State University, University Park, PA 16801, USA.
authors.forename: S A
authors.initials: SA
authors.lastname: Racunas
authors.forename: N H
authors.initials: NH
authors.lastname: Shah
authors.forename: I
authors.initials: I
authors.lastname: Albert
authors.forename: N V
authors.initials: NV
authors.lastname: Fedoroff
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005690:Galactose / Q000378:metabolism*; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D010865:Pilot Projects; D012107:Research Design; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D018511:Systems Integration
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D005690:Galactose