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Synthetic Biology Open Language

Abbreviation: SBOL

General Information

The Synthetic Biology Open Language (SBOL) is a standard used for the in silico representation of genetic designs. SBOL is designed to allow synthetic biologists and genetic engineers to electronically exchange designs, send and receive genetic designs to and from biofabrication centres, facilitate storage of genetic designs in repositories, and embed genetic designs in publications.

Homepage https://sbolstandard.org/

Countries that developed this resource Canada , India , Japan , Latvia , Panama , Switzerland , United Kingdom , United States

Created in 2009

Taxonomic range

All

Knowledge Domains

Subjects

User-defined Tags

Data sharing

How to cite this record FAIRsharing.org: SBOL; Synthetic Biology Open Language; DOI: https://doi.org/10.25504/FAIRsharing.cwf4py; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Oct 26 2021 8:58 a.m.

This record is maintained by mgaldzic ORCID and sboleditors

Record updated: June 23, 2021, 11:44 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.cwf4py' by 'The FAIRsharing Team' at 11:44, 23 Jun 2021 (approved):

	'related_standards' has been modified:
		Before:
			Synthetic Biology Open Language Visual
			Minimal Information Required In the Annotation of Models
			FASTA Sequence Format
			GenBank Sequence Format
		After:
			Synthetic Biology Open Language Visual
			Minimal Information Required In the Annotation of Models
			FASTA Sequence Format
			GenBank Sequence Format
			RDF/XML Syntax Specification
			JavaScript Object Notation for Linking Data
			Terse RDF Triple Language
		Added:
			RDF/XML Syntax Specification
			JavaScript Object Notation for Linking Data
			Terse RDF Triple Language
		Removed:

	'supportLinks' has been modified:
		Before:
			contact form|https://sbolstandard.org/contact/
			forum|https://groups.google.com/g/sbol-dev
			forum|https://github.com/SynBioDex/SBOL-specification/issues
			help|https://sbolstandard.org/datamodel-examples/
			online documentation|https://sbolstandard.org/datamodel-about/
			online documentation|https://github.com/SynBioDex/SBOL-specification
		After:
			FAQ|https://sbolstandard.org/faq/
			contact form|https://sbolstandard.org/contact/
			forum|https://groups.google.com/g/sbol-dev
			forum|https://github.com/SynBioDex/SBOL-specification/issues
			help|https://sbolstandard.org/datamodel-examples/
			online documentation|https://github.com/SynBioDex/SBOL-specification
			online documentation|https://sbolstandard.org/datamodel-about/
		Added:
			FAQ|https://sbolstandard.org/faq/
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.cwf4py' by 'The FAIRsharing Team' at 11:39, 23 Jun 2021 (approved):

	'related_standards' has been modified:
		Before:
			Synthetic Biology Open Language Visual
			Minimal Information Required In the Annotation of Models
		After:
			Synthetic Biology Open Language Visual
			Minimal Information Required In the Annotation of Models
			FASTA Sequence Format
			GenBank Sequence Format
		Added:
			FASTA Sequence Format
			GenBank Sequence Format
		Removed:

	'dataProcesses' has been modified:
		Before:
			Browse ontology, data access, https://dissys.github.io/sbol-owl/sbol-owl.html
		After:
			Browse ontology, data access, https://dissys.github.io/sbol-owl/sbol-owl.html
			Download Specification, data release, https://sbolstandard.org/datamodel-specification/
		Added:
			Download Specification, data release, https://sbolstandard.org/datamodel-specification/
		Removed:

	'supportLinks' has been modified:
		Before:
			FAQ|http://sbolstandard.org/faq/
			email|editors@sbolstandard.org
			forum|https://groups.google.com/forum/#!forum/sbol-dev
			online documentation|https://sbolstandard.org/data-model-specification/
		After:
			contact form|https://sbolstandard.org/contact/
			forum|https://groups.google.com/g/sbol-dev
			forum|https://github.com/SynBioDex/SBOL-specification/issues
			help|https://sbolstandard.org/datamodel-examples/
			online documentation|https://sbolstandard.org/datamodel-about/
			online documentation|https://github.com/SynBioDex/SBOL-specification
		Added:
			contact form|https://sbolstandard.org/contact/
			forum|https://groups.google.com/g/sbol-dev
			forum|https://github.com/SynBioDex/SBOL-specification/issues
			help|https://sbolstandard.org/datamodel-examples/
			online documentation|https://sbolstandard.org/datamodel-about/
			online documentation|https://github.com/SynBioDex/SBOL-specification
		Removed:
			FAQ|http://sbolstandard.org/faq/
			email|editors@sbolstandard.org
			forum|https://groups.google.com/forum/#!forum/sbol-dev
			online documentation|https://sbolstandard.org/data-model-specification/

	'publications' has been modified:
		Before:
			The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. |Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grnberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM|Nature Biotechnology|2014
			Proposed data model for the next version of the Synthetic Biology Open Language|Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ|ACS Synth Biol.|2014
		After:
			The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. |Galdzicki M, Clancy KP, Oberortner E et al.|Nature Biotechnology|2014
			Proposed data model for the next version of the Synthetic Biology Open Language|Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ|ACS Synth Biol.|2014
		Added:
			The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. |Galdzicki M, Clancy KP, Oberortner E et al.|Nature Biotechnology|2014
		Removed:
			The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. |Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grnberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM|Nature Biotechnology|2014

	'onto_domains' has been modified:
		Before:
			DNA sequence
			Nucleic acid design
			Sequence annotation
		After:
			DNA sequence
			Nucleic acid design
			Sequence annotation
			modeling and simulation objective
		Added:
			modeling and simulation objective
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.cwf4py' by 'The FAIRsharing Team' at 18:50, 09 Feb 2020 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|http://sbolstandard.org/faq/
			email|editors@sbolstandard.org
			forum|https://groups.google.com/forum/#!forum/sbol-dev
			online documentation|http://www.sbolstandard.org/initiatives/serialization
			online documentation|http://sbolstandard.org/downloads/specification-data-model-2-0/
			online documentation|http://sbolstandard.org/downloads/specification-sbol-visual/
		After:
			FAQ|http://sbolstandard.org/faq/
			email|editors@sbolstandard.org
			forum|https://groups.google.com/forum/#!forum/sbol-dev
			online documentation|https://sbolstandard.org/data-model-specification/
		Added:
			online documentation|https://sbolstandard.org/data-model-specification/
		Removed:
			online documentation|http://www.sbolstandard.org/initiatives/serialization
			online documentation|http://sbolstandard.org/downloads/specification-data-model-2-0/
			online documentation|http://sbolstandard.org/downloads/specification-sbol-visual/

	'dataProcesses' has been modified:
		Before:
		After:
			Browse ontology
		Added:
			Browse ontology
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.cwf4py' by 'The FAIRsharing Team' at 18:42, 09 Feb 2020 (approved):

	'user_defined_tags' has been modified:
		Before:
		After:
			Data sharing
			Data standards
		Added:
			Data sharing
			Data standards
		Removed:

	'miriam_id' has been modified:
		Before: None
		After: 

	'homepage' has been modified:
		Before: http://www.sbolstandard.org/
		After: https://sbolstandard.org/

In Collections

Computational Modeling (COMBINE)

The NormSys Registry for Modeling Standards

ISO/CD 20691 Collection - DRAFT

Systems Medicine

Support

General

FAQ	FAQ
contact form	Contact Information
forum	SBOL Developer List
forum	GitHub Issue Tracker
help	Examples
online documentation	Github Repository
online documentation	About

Additional Information

Contact

SBOL Editors

Tools

SBOL Validator	https://validator.sbolstandard.org/
SBOL Converter	https://converter.sbolstandard.org/
Synthetic Biology Software Tools	https://sbolstandard.org/applications/
SBOL Libraries	https://sbolstandard.org/libraries/

Schemas

Name: SBOL
Version: 0

Download

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Creative Commons Attribution 4.0 International (CC BY 4.0)

Data Release

Download Specification

https://sbolstandard.org/datamodel-specification/

Data Access

Browse ontology

https://dissys.github.io/sbol-owl/sbol-owl.html

Publications

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Galdzicki M, Clancy KP, Oberortner E et al.
Nature Biotechnology 2014

View Paper (PubMed) View Publication

Proposed data model for the next version of the Synthetic Biology Open Language

Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ
ACS Synth Biol. 2014

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Minimal Information Required In the Annotation of Models

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (3)

Virtual Parts Repository
The Virtual Parts Repository (VPR) is a repository of reusable, modular and composable models of biological parts.

iGEM Registry of Standard Biological Parts
The iGEM Parts Registry is a growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. As part of the synthetic biology community's efforts to make biology easier to engineer, it provides a source of genetic parts to iGEM teams and academic labs. You can learn more about iGEM Teams and Labs at iGEM.org.

SynBioHub
SynBioHub is a design repository for people designing biological constructs. It enables DNA and protein designs to be uploaded, then provides a shareable link to allow others to view them. SynBioHub also facilitates searching for information about existing useful parts and designs by combining data from a variety of sources.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by mgaldzic ORCID and sboleditors

Funds

Engineering and Physical Sciences Research Council (EPSRC), UK (Government body)
Agilent Technologies (Company)
Defense Advanced Research Projects Agency (Government body)
National Science Foundation (NSF), USA (Government body)
National Human Genome Research Institute (NHGRI), Bethesda, MD, USA (Government body)

Maintains

COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)
U.S. National Library of Medicine (Government body)
SBOL Developers (Consortium)

Grant Number(s)

1355909 (National Science Foundation (NSF), USA)
1356401 (National Science Foundation (NSF), USA)
EP/J02175X/1 (Engineering and Physical Sciences Research Council (EPSRC), UK)

Synthetic Biology Open Language

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	sbol.xsd
	rdf.xsd