Synthetic Biology Open Language

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

Normative definitions

SBOL is defined in a set of specification documents that describe the elements of the language, its syntax, and validation rules. SBOL Visual is a set of symbols to represent graphically constructs described in SBOL

The latest specifications are:

Governance

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

Communication

SBOL 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 group, contact the SBOL Editors at editors@sbolstandard.org.

To join the SBOL Visual Working Group, contact visual@sbolstandard.org.

Software support

Many software tools support SBOL, including SBOL APIs, SBOL helper tools and end user software supporting SBOL.

Contact

For information about SBOL, contact editors@sbolstandard.org.

How to cite SBOL

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

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.

SBOL Visual was conceived and presented as an RFC in 2010, inspired by the need to represent designs in software user interfaces. SBOL Visual 1.0.0 was published as an RFC in 2013, providing a cleaner symbol set and more formalized symbol definitions via the Sequence Ontology.

The development of SBOL 2.0 and corresponding visual notation is currently underway. To join the discussion, contact the editors at editors@sbolstandard.org.