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The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering

Lookup NU author(s): James Alastair McLaughlin McLaughlin, Dr Goksel Misirli, Professor Anil Wipat

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

© Copyright © 2020 McLaughlin, Beal, Mısırlı, Grünberg, Bartley, Scott-Brown, Vaidyanathan, Fontanarrosa, Oberortner, Wipat, Gorochowski and Myers.The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings. Here, we introduce the SBOL3 specification both in comparison to previous versions of SBOL and through practical examples of its use.


Publication metadata

Author(s): McLaughlin JA, Beal J, Misirli G, Grunberg R, Bartley BA, Scott-Brown J, Vaidyanathan P, Fontanarrosa P, Oberortner E, Wipat A, Gorochowski TE, Myers CJ

Publication type: Article

Publication status: Published

Journal: Frontiers in Bioengineering and Biotechnology

Year: 2020

Volume: 8

Online publication date: 11/09/2020

Acceptance date: 31/07/2020

Date deposited: 12/01/2021

ISSN (electronic): 2296-4185

Publisher: Frontiers Media S.A.

URL: https://doi.org/10.3389/fbioe.2020.01009

DOI: 10.3389/fbioe.2020.01009


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Funding

Funder referenceFunder name
1939892
1522074
BB/L01386X/1
CCF-1748200
EP/N031962/1EPSRC
EP/R019002/1EPSRC
EP/J02175X/1
FA8750-17-C-0229
FA875017CO184
FUJIFILM DioSynth Biotechnologies
EP/L016494/1
EP/R003629/1EPSRC
UF160357

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