HyBrow: a prototype system for computer-aided hypothesis evaluation
Abstract
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
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A common, inclusive and computable pathway data language is necessary to share knowledge about pathway maps and facilitate integration and use for hypothesis testing in biology.
“A common, inclusive and computable pathway data language is necessary to share knowledge about pathway maps and to facilitate integration and use for hypothesis testing in biology24.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [24]
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The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · see citing works
“For instance, visualization and analysis tools developed for one pathway database cannot be reused for others, making software development efforts more expensive.”
Self-citation
- Authors
- Racunas, S. A., Shah, N. H., Albert, I., & Fedoroff, N. V.
- Affiliations
- Pennsylvania State University (US)
- Corresponding author
- Racunas, S. A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-08-04
- Volume
- 20
- Issue
- suppl_1
- Pages
- i257-i264
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2120702690
- Cited by
- 70
- References
- 30
- Citations by year
- 2024: 1 · 2022: 1 · 2021: 3 · 2019: 1 · 2018: 2 · 2017: 1 · 2016: 3 · 2015: 4 · 2014: 5 · 2013: 5 · 2012: 5
- FWCI
- 1.18
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- hypothesis evaluation, biological process modeling, biological data integration, Saccharomyces cerevisiae, bioinformatics software
- MeSH terms
- Galactose, Models, Biological, Pilot Projects, Research Design, Saccharomyces cerevisiae, Information Storage and Retrieval, Systems Integration, Computational Biology, Saccharomyces cerevisiae Proteins, Databases, Protein
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