SBOL converter: enabling backward compatibility for biological designs
Metehan Ünal, Chris J. Myers, Ihsan Tolga Medeni, Jacob Beal, Prashant Vaidyanathan, Lukas Buecherl, Felipe Buson, Georgie Hau Sørensen, Gonzalo Vidal, Carolus Vitalis, Erik Kubaczka, Roberto Galizi, Göksel MısırlıAbstract
The Synthetic Biology Open Language (SBOL) is a community-driven and machine-readable standard for creating and sharing biological designs. SBOL has evolved over the years, resulting in three major versions, each introducing new features. Although SBOL3 is the latest community-adopted version, it has not been fully integrated into software tools and repositories due to the lack of essential libraries to facilitate this transition. In this paper, we present the SBOL Converter, a backward-compatibility tool that can update legacy designs to the latest SBOL version. Designs can also be converted to previous versions to allow legacy tools to be used in ongoing projects. Moreover, it incorporates existing SBOL tools, providing a unified interface to orchestrate the validation of designs and checking against various compliance rules and best practices. The converter can also process other popular biological formats such as GenBank and FASTA. As a lightweight tool, it can be integrated into engineering biology design workflows to accelerate tool development and enable the transition to the latest versions as they are released, facilitating the reusability and reproducibility of biological designs.