Synthetic Biology Open Language Data Model

SBOL The Synthetic Biology Open Language Data (SBOL Data) Model is an open standard designed to facilitate the exchange and storage of genetic designs. Through its core data model, SBOL aims to allow researchers to unambiguously share information about the structure and intended behavior of designed biological constructs.

Normative definitions

SBOL data is defined in a set of specification documents that describe the elements of the language, its syntax, and validation rules.

The latest specifications are:

Governance

SBOL Data development is coordinated by an editorial board and the chair elected by the community.

Communication

SBOL data development is executed by the SBOL Developers Group through discussion on the group mailing list, in virtual meetings, and at biannual in-person workshops.

To join the SBOL Developers Group, contact the SBOL Editors.

Software support

Many software tools support SBOL data, including SBOL APIs, SBOL Converter/Validator tools and end user software supporting SBOL Data.

Contact

For information about SBOL Data, contact the SBOL Editors.

How to cite SBOL Data

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, Grünberg 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. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology (2014), 32: 545-550. http://identifiers.org/pubmed/24911500

Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T. Sharing structure and function in biological design with SBOL 2.0. ACS synthetic biology. 2016 May 4;5(6):498-506. http://pubs.acs.org/doi/abs/10.1021/acssynbio.5b00215

Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C. Synthetic Biology Open Language (SBOL) Version 2.1. 0. Journal of Integrative Bioinformatics. 2016 Sep 1;13(3):30-132. https://www.degruyter.com/view/j/jib.2016.13.issue-3/biecoll-jib-2016-291/biecoll-jib-2016-291.xml

History

A significant issue in synthetic biology is the difficulty in reproducing published synthetic designs. This prompted the development of SBOL to be started in 2007/2008. SBOL allows researchers and engineers to unambiguously exchange synthetic biology designs, that includes at the core the ability to describe a design in terms of DNA. Extensions permit other information to be represented. The language is based on RDF/XML. XML was chosen since it allows schemas to be specified and permits easier integration with other standards. SBOL also allows users to integrate existing biological information, such as the use of existing ontology terms for genetic design components.

SBOL was initially announced under the name “PoBoL” (Provisional BioBrick Language) in 2008 as a result of seed funding from Microsoft. SBOL version 1.0.0 was published in 2011, and includes the ability to specify hierarchical genetic designs, either partial or complete. SBOL was updated to version 1.1.0 in 2012.

The development of SBOL 2.0 is currently underway. To join the discussion, contact the SBOL Editors.