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

dc.contributor.authorMcLaughlin, James Alastair
dc.contributor.authorBeal, Jacob
dc.contributor.authorMısırlı, Göksel
dc.contributor.authorGrunberg, Raik
dc.contributor.authorBartley, Bryan A.
dc.contributor.authorScott-Brown, James
dc.contributor.authorVaidyanathan, Prashant
dc.contributor.authorFontanarrosa, Pedro
dc.contributor.authorOberortner, Ernst
dc.contributor.authorWipat, Anil
dc.contributor.authorGorochowski, Thomas E.
dc.contributor.authorMyers, Chris J.
dc.date.accessioned2020-10-04T12:47:23Z
dc.date.available2020-10-04T12:47:23Z
dc.date.issued2020-09-11
dc.date.submitted2020-05-29
dc.identifier.citationMcLaughlin, J. A., Beal, J., Mısırlı, G., Grünberg, R., Bartley, B. A., Scott-Brown, J., … Myers, C. J. (2020). The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. Frontiers in Bioengineering and Biotechnology, 8. doi:10.3389/fbioe.2020.01009
dc.identifier.issn2296-4185
dc.identifier.doi10.3389/fbioe.2020.01009
dc.identifier.urihttp://hdl.handle.net/10754/665428
dc.description.abstractThe 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.
dc.description.sponsorshipIn addition to the listed authors, the development of SBOL3 has benefited greatly from discussions with many stakeholders throughout the user and developer community, including the SBOL developers mailing list, users and developers of the SBOL libraries and SBOL-enabled software tools, and the SBOL Industrial Consortium. Valuable support and guidance was also provided by members of the SBOL Editors and SBOL Steering Committee.
dc.publisherFrontiers Media SA
dc.relation.urlhttps://www.frontiersin.org/article/10.3389/fbioe.2020.01009/full
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleThe Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.identifier.journalFrontiers in Bioengineering and Biotechnology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionSchool of Computing, Newcastle University, Newcastle-upon-Tyne, United Kingdom
dc.contributor.institutionRaytheon BBN Technologies, Cambridge, MA, United States
dc.contributor.institutionSchool of Mathematics and Computing, Keele University, Keele, United Kingdom
dc.contributor.institutionNuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
dc.contributor.institutionMicrosoft Research, Cambridge, United Kingdom
dc.contributor.institutionDepartment of Biomedical Engineering, University of Utah, Salt Lake City, UT, United States
dc.contributor.institutionLawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
dc.contributor.institutionSchool of Biological Sciences, University of Bristol, Bristol, United Kingdom
dc.contributor.institutionDepartment of Electrical, Computer, and Energy Engineering, University of Colorado, Boulder, CO, United States
dc.identifier.volume8
kaust.personGrunberg, Raik
dc.date.accepted2020-07-31
dc.identifier.eid2-s2.0-85091506203
refterms.dateFOA2020-10-04T12:48:31Z


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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Except where otherwise noted, this item's license is described as This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.