Synthetic Biology Open Language (SBOL) Version 2.3

Curtis Madsen, Angel Goñi Moreno, Umesh P, Zachary Palchick, Nicholas Roehner, Christian Atallah, Bryan Bartley, Kiri Choi, Robert Sidney Cox, Thomas Gorochowski, Raik Grünberg, Chris Macklin, James McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew Pocock, Meher Samineni, James Scott-Brown, Ysis Tarter, Michael ZhangZhen Zhang, Zach Zundel, Jacob Beal, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris Myers, Ernst Oberortner, Herbert Sauro, Anil Wipat

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Abstract

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems is to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.3.0 of SBOL, which builds upon version 2.2.0 published in last year’s JIB Standards in Systems Biology special issue. In particular, SBOL 2.3.0 includes means of succinctly representing sequence modifications, such as insertion, deletion, and replacement, an extension to support organization and attachment of experimental data derived from designs, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, refinement of a number of validation rules, improved figures and examples, and clarification on a number of issues related to the use of external ontology terms.
Original languageEnglish
Article number20190025
Number of pages150
JournalJournal of Integrative Bioinformatics
DOIs
Publication statusPublished - 13 Jun 2019

Structured keywords

  • BrisSynBio
  • Bristol BioDesign Institute

Keywords

  • Synthetic Biology
  • Synthetic Biology Open Language
  • Standards

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  • Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1

    Madsen, C., Goni Moreno, A., Palchick, Z., P, U., Roehner, N., Bartley, B., Bhatia, S., Bhakta, S., Bissell, M., Clancy, K., Cox, R. S., Gorochowski, T., Grunberg, R., Luna, A., McLaughlin, J., Nguyen, T., Le Novere, N., Pocock, M., Sauro, H., Scott-Brown, J. & 8 others, Sexton, J. T., Stan, G-B., Tabor, J. J., Voigt, C. A., Zundel, Z., Myers, C., Beal, J. & Wipat, A., 13 Jun 2019, In: Journal of Integrative Bioinformatics. 78 p., 20180101.

    Research output: Contribution to journalArticle (Academic Journal)peer-review

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    6 Citations (Scopus)
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