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Updated: Jul 1, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Standards and ontologies in computational systems biology.
Herbert M Sauro1, Frank T Bergmann
1Department of Bioengineering, William H. Foege Building, Seattle, WA 98195-5061, U.S.A. hsauro@u.washington.edu
Essays in Biochemistry
|September 17, 2008
Summary
Systems biology relies on computational models. This chapter details Systems Biology Markup Language (SBML) and CellML, key standards for exchanging these models between software, aiding biological research.
Area of Science:
- Computational systems biology
- Bioinformatics
- Scientific modeling
Background:
- The increasing reliance on computational models in systems biology necessitates standardized methods for model exchange.
- Biologists require tools to easily share models across different software platforms.
- Lack of standardization hinders model reproducibility and collaboration.
Purpose of the Study:
- To describe prominent model interchange standards in systems biology.
- To discuss related advancements in model annotation, ontologies, and visualization.
- To introduce software tools supporting model development and editing.
Main Methods:
- Review and description of Systems Biology Markup Language (SBML).
- Review and description of CellML.
- Discussion of visual layout initiatives, ontologies, and annotation best practices.
- Introduction to relevant software tools and libraries.
Main Results:
- SBML and CellML are presented as chief standards for biological model exchange.
- Related initiatives like ontologies and annotation best practices are discussed.
- Software tools for model development and visualization are introduced.
Conclusions:
- Standardized model interchange languages like SBML and CellML are crucial for systems biology.
- Further development in visualization and annotation will enhance model usability.
- These advancements facilitate collaboration and reproducibility in computational biology.
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