The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering
Abstract
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.
- Authors:
-
- Newcastle Univ. (United Kingdom)
- Raytheon BBN Technologies, Cambridge, MA (United States)
- Keele Univ. (United Kingdom)
- King Abdullah Univ.y of Science and Technology (Saudi Arabia)
- Univ. of Oxford (United Kingdom)
- Microsoft Research, Cambridge (United Kingdom)
- Univ. of Utah, Salt Lake City, UT (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Bristol (United Kingdom)
- Univ. of Colorado, Boulder, CO (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1706643
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Bioengineering and Biotechnology
- Additional Journal Information:
- Journal Volume: 8; Journal ID: ISSN 2296-4185
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; synthetic biology; data standards; data exchange; knowledge representation; SBOL
Citation Formats
McLaughlin, James Alastair, Beal, Jacob, Mısırlı, Göksel, Grünberg, Raik, Bartley, Bryan A, Scott-Brown, James, Vaidyanathan, Prashant, Fontanarrosa, Pedro, Oberortner, Ernst, Wipat, Anil, Gorochowski, Thomas E., and Myers, Chris J. The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. United States: N. p., 2020.
Web. doi:10.3389/fbioe.2020.01009.
McLaughlin, James Alastair, Beal, Jacob, Mısırlı, Göksel, Grünberg, Raik, Bartley, Bryan A, Scott-Brown, James, Vaidyanathan, Prashant, Fontanarrosa, Pedro, Oberortner, Ernst, Wipat, Anil, Gorochowski, Thomas E., & Myers, Chris J. The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. United States. https://doi.org/10.3389/fbioe.2020.01009
McLaughlin, James Alastair, Beal, Jacob, Mısırlı, Göksel, Grünberg, Raik, Bartley, Bryan A, Scott-Brown, James, Vaidyanathan, Prashant, Fontanarrosa, Pedro, Oberortner, Ernst, Wipat, Anil, Gorochowski, Thomas E., and Myers, Chris J. Fri .
"The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering". United States. https://doi.org/10.3389/fbioe.2020.01009. https://www.osti.gov/servlets/purl/1706643.
@article{osti_1706643,
title = {The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering},
author = {McLaughlin, James Alastair and Beal, Jacob and Mısırlı, Göksel and Grünberg, Raik and Bartley, Bryan A and Scott-Brown, James and Vaidyanathan, Prashant and Fontanarrosa, Pedro and Oberortner, Ernst and Wipat, Anil and Gorochowski, Thomas E. and Myers, Chris J.},
abstractNote = {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.},
doi = {10.3389/fbioe.2020.01009},
journal = {Frontiers in Bioengineering and Biotechnology},
number = ,
volume = 8,
place = {United States},
year = {Fri Sep 11 00:00:00 EDT 2020},
month = {Fri Sep 11 00:00:00 EDT 2020}
}
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