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Updated: Jul 27, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems
D L Cook1, J F Farley, S J Tapscott
1Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA. raintown@halcyon.com
Genome Biology
|April 18, 2001
Summary
A new graphical description language, BioD, is proposed for systems biology to archive and analyze complex biological functions. This internet-based system uses a limited icon set to model cell biology, proving feasible for functional analysis.
Area of Science:
- Systems Biology
- Computational Biology
- Bioinformatics
Background:
- Complex biological functions in health and disease require advanced description and analysis methods.
- Existing methods may not adequately capture the intricacies of biological systems.
Purpose of the Study:
- To propose a computerized, internet-based graphical description language for systems biology.
- To explore the utility and feasibility of such a language for functional biology analysis.
Main Methods:
- Conceptual basis for designing a graphical description language.
- Development of BioD, a prototype language.
- Demonstration using example models of cell-biological systems.
Main Results:
- A limited lexicon of icons and arrows is sufficient for describing complex cell-biological systems.
- Discrete models can be posted and linked on the internet.
- BioD demonstrates the feasibility of this approach.
Conclusions:
- BioD can be implemented as an extensible, multidisciplinary language using current technology.
- It serves to archive functional systems knowledge.
- It supports both qualitative and quantitative functional analysis.
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