title: Proposed data model for the next version of the synthetic biology open language.
abstract: 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.
authors.affiliation: Department of Bioengineering, University of Utah , Salt Lake City, Utah, United States.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Roehner
authors.forename: Ernst
authors.initials: E
authors.lastname: Oberortner
authors.forename: Matthew
authors.initials: M
authors.lastname: Pocock
authors.forename: Jacob
authors.initials: J
authors.lastname: Beal
authors.forename: Kevin
authors.initials: K
authors.lastname: Clancy
authors.forename: Curtis
authors.initials: C
authors.lastname: Madsen
authors.forename: Goksel
authors.initials: G
authors.lastname: Misirli
authors.forename: Anil
authors.initials: A
authors.lastname: Wipat
authors.forename: Herbert
authors.initials: H
authors.lastname: Sauro
authors.forename: Chris J
authors.initials: CJ
authors.lastname: Myers
mesh_terms: D000818:Animals; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D003198:Computer Simulation; D006224:Cricetinae; D005818:Genetic Engineering; D008954:Models, Biological; D008957:Models, Genetic; D011381:Programming Languages; D012093:Replicon / Q000235:genetics; D012984:Software; D058615:Synthetic Biology / Q000706:statistics & numerical data*
keywords: SBOL; modular design; standards; synthetic biology