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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language
Tramy Nguyen, Nicholas Roehner1, Zach Zundel
1Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.
Abstract:
Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.
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