ShortBOL: a shorthand textual language to create SBOL designs quickly and easily

Synthetic Biology Open Language (SBOL) is an open standard for the representation of in silico biological designs, facilitating computational design, exchange, and reproducibility of biological systems. SBOL uses RDF/XML serialization to express RDF graphs as an XML documents. Although this syntax is ideal for precise machine communication, SBOL RDF/XML is rather complex for humans to manually edit designs, especially those involving many components and features. Because of this, several software tools have been developed to manipulate SBOL, such as libSBOL and pySBOL for reading, writing, and constructing genetic designs according to the standardized specifications of SBOL. Nevertheless, these tools still require the use of strong programming skills, and there is need for a lightweight SBOL scripting language to bridge the gap between manual editing, visual design and direct use of libraries.

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Responding to this need, ShortBOL has been developed. ShortBOL is a human readable/writable shorthand for describing biological designs in SBOL, and it has been developed for those familiar with the SBOL data model but that wish to rapidly sketch synbio designs using a simple language instead of writing code. ShortBOL is not intended to replace SBOL, however, which can represent additional complex design information, and is based on RDF, meaning it can benefit from existing Semantic Web tooling. ShortBOL is currently built around a minimal selection of language constructs, so there is a further need for future development of ShortBOL to support more complex features of the SBOL data model (i.e. capturing the lineage of designs, combinatorial assembly, or encoding parameters and measures) and to use a syntax that is more commonplace in the synthetic biology community. The development of a new version that includes this as well as a fully online editor and expansion pipeline is currently ongoing. Check out the open access paper by Crowther et al. 2020 for more information on ShortBOL.

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