Proposed data model for the next version of the synthetic biology open language

ACS Synth Biol. 2015 Jan 16;4(1):57-71. doi: 10.1021/sb500176h. Epub 2014 Jun 16.


While the first version of the Synthetic Biology Open Language (SBOL) has been adopted by several academic and commercial genetic design automation (GDA) software tools, it only covers a limited number of the requirements for a standardized exchange format for synthetic biology. In particular, SBOL Version 1.1 is capable of representing DNA components and their hierarchical composition via sequence annotations. This proposal revises SBOL Version 1.1, enabling the representation of a wider range of components with and without sequences, including RNA components, protein components, small molecules, and molecular complexes. It also introduces modules to instantiate groups of components on the basis of their shared function and assert molecular interactions between components. By increasing the range of structural and functional descriptions in SBOL and allowing for their composition, the proposed improvements enable SBOL to represent and facilitate the exchange of a broader class of genetic designs.

Keywords: SBOL; modular design; standards; synthetic biology.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Computer Simulation
  • Cricetinae
  • Genetic Engineering
  • Models, Biological*
  • Models, Genetic
  • Programming Languages
  • Replicon / genetics
  • Software
  • Synthetic Biology / statistics & numerical data*