Proposed Data Model for the Next Version of the Synthetic Biology Open Language

Nicholas Roehner; Ernst Oberortner; Matthew Pocock; Jacob Beal; Kevin Clancy; Curtis Madsen; Goksel Misirli; Anil Wipat; Herbert Sauro; Chris J. Myers

doi:10.1021/sb500176h

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Proposed Data Model for the Next Version of the Synthetic Biology Open Language

Journal article

Peer reviewed

Proposed Data Model for the Next Version of the Synthetic Biology Open Language

Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Jacob Beal, Kevin Clancy, Curtis Madsen, Goksel Misirli, Anil Wipat, Herbert Sauro and Chris J. Myers

ACS synthetic biology, Vol.4(1), pp.57-71

01/16/2015

DOI: 10.1021/sb500176h

PMID: 24896221

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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.

Biochemical Research Methods

Biochemistry & Molecular Biology

Life Sciences & Biomedicine

Science & Technology

Details

Title: Subtitle: Proposed Data Model for the Next Version of the Synthetic Biology Open Language
Creators: Nicholas Roehner - University of Utah
Ernst Oberortner - Boston University
Matthew Pocock - Newcastle University
Jacob Beal - RTX
Kevin Clancy - Life Technol, Carlsbad, CA USA
Curtis Madsen - University of Newcastle Australia
Goksel Misirli - Newcastle University
Anil Wipat - Newcastle University
Herbert Sauro - University of Washington
Chris J. Myers - University of Utah
Resource Type: Journal article
Publication Details: ACS synthetic biology, Vol.4(1), pp.57-71
Publisher: Amer Chemical Soc
DOI: 10.1021/sb500176h
PMID: 24896221
ISSN: 2161-5063
eISSN: 2161-5063
Number of pages: 15
Grant note: CCF-1218095 / National Science Foundation; National Science Foundation (NSF)
Language: English
Date published: 01/16/2015
Academic Unit: Electrical and Computer Engineering
Record Identifier: 9984627287802771

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