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

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.

doi:10.3389/fbioe.2020.01009

Title: 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:

McLaughlin, James Alastair ^[1]; Beal, Jacob ^[2]; Mısırlı, Göksel ^[3]; Grünberg, Raik ^[4]; Bartley, Bryan A ^[2]; Scott-Brown, James ^[5]; Vaidyanathan, Prashant ^[6]; Fontanarrosa, Pedro ^[7]; Oberortner, Ernst ^[8]; Wipat, Anil ^[1]; Gorochowski, Thomas E. ^[9]; Myers, Chris J. ^[10]

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:: Fri Sep 11 00:00:00 EDT 2020

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.

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                    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

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                    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.

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

Abstract

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Towards programming languages for genetic engineering of living cells journal, April 2009

SBOL Visual 2 Ontology journal, March 2020

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PubChemRDF: towards the semantic annotation of PubChem compound and substance databases journal, July 2015

Model annotation for synthetic biology: automating model to nucleotide sequence conversion journal, February 2011

Maintaining knowledge about temporal intervals journal, November 1983

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Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs journal, May 2016

Synthetic Biology Open Language (SBOL) Version 2.0.0 text, January 2015

Sharing Structure and Function in Biological Design with SBOL 2.0 journal, May 2016

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DeviceEditor visual biological CAD canvas journal, December 2012

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SBOL Visual: A Graphical Language for Genetic Designs journal, December 2015

ChEBI: a database and ontology for chemical entities of biological interest journal, December 2007

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems journal, April 2011

Pigeon: A Design Visualizer for Synthetic Biology journal, March 2013

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models journal, March 2003

i B io S im 3: A Tool for Model-Based Genetic Circuit Design journal, June 2018

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A Framework for Genetic Logic Synthesis journal, November 2015

Communicating Structure and Function in Synthetic Biology Diagrams journal, July 2019

DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data journal, October 2016

A Rule-Based Design Specification Language for Synthetic Biology
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Organizing genome engineering for the gigabase scale
journal, February 2020

ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)
journal, March 2020

The Gene Ontology (GO) database and informatics resource
journal, January 2004

Synthetic Biology Open Language (SBOL) Version 2.2.0
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Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems
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SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology
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The BioPAX community standard for pathway data sharing
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Streamlining the Design-to-Build Transition with Build-Optimization Software Tools
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Synthetic Biology Open Language (SBOL) Version 2.1.0
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Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts
conference, May 2014

GenBank
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j5 DNA Assembly Design Automation Software
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Foundations for engineering biology
journal, November 2005

Genetic circuit design automation
journal, March 2016

Composable Modular Models for Synthetic Biology
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Towards programming languages for genetic engineering of living cells
journal, April 2009

SBOL Visual 2 Ontology
journal, March 2020

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
journal, June 2014

Synthetic Biology Open Language (SBOL) Version 2.3
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SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information
journal, May 2019

A Computational Workflow for the Automated Generation of Models of Genetic Designs
journal, May 2018

SBOLDesigner 2: An Intuitive Tool for Structural Genetic Design
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Interactive assembly algorithms for molecular cloning
journal, April 2014

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1
journal, June 2019

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases
journal, July 2015

Model annotation for synthetic biology: automating model to nucleotide sequence conversion
journal, February 2011

Maintaining knowledge about temporal intervals
journal, November 1983

Synthetic biology open language (SBOL) version 3.0.0
journal, June 2020

Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs
journal, May 2016

Synthetic Biology Open Language (SBOL) Version 2.0.0
text, January 2015

Sharing Structure and Function in Biological Design with SBOL 2.0
journal, May 2016

Controlled vocabularies and semantics in systems biology
journal, January 2011

DeviceEditor visual biological CAD canvas
journal, December 2012

Construction of a genetic toggle switch in Escherichia coli
journal, January 2000

SBOL Visual: A Graphical Language for Genetic Designs
journal, December 2015

ChEBI: a database and ontology for chemical entities of biological interest
journal, December 2007

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems
journal, April 2011

Pigeon: A Design Visualizer for Synthetic Biology
journal, March 2013

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
journal, March 2003

i B io S im 3: A Tool for Model-Based Genetic Circuit Design
journal, June 2018

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools
journal, June 2012

A Framework for Genetic Logic Synthesis
journal, November 2015

Communicating Structure and Function in Synthetic Biology Diagrams
journal, July 2019

DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data
journal, October 2016