libSBOLj3: a graph-based library for design and data exchange in synthetic biology.

Mısırlı, Göksel

Abstract

The Synthetic Biology Open Language version 3 data standard provides a graph-based approach to exchange information about biological designs. The new data model has major updates and offers several features for software tools. Here, we present libSBOLj3 to facilitate data exchange and provide interoperability between computer-aided design and automation tools using this standard. The library adopts a graph-based approach. Tool developers can extend these graphs with application-specific information and use detailed validation reports to identify errors and interoperability issues and apply best practice rules. The libSBOLj3 library is implemented in Java and can be downloaded or used as a Maven dependency. The open-source project, code examples and documentation about accessing and using the library are available via GitHub at https://github.com/SynBioDex/libSBOLj3. [Abstract copyright: © The Author(s) 2023. Published by Oxford University Press.]

• Journal Article Type: Article
• Acceptance Date: Aug 23, 2023
• Online Publication Date: Aug 25, 2023
• Publication Date: Aug 1, 2023
• Deposit Date: Sep 4, 2023
• Publicly Available Date: Sep 6, 2023
• Journal: Bioinformatics
• Print ISSN: 1367-4803
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 39
• Issue: 8
• Article Number: btad525
• Pages: 3
• DOI: https://doi.org/10.1093/bioinformatics/btad525
• Keywords: Computational Mathematics; Computational Theory and Mathematics; Computer Science Applications; MolecularSynthetic Biology; Biochemistry; Statistics and Probability, Gene Library, Language, Automation, Documentation
• Publisher URL: https://academic.oup.com/bioinformatics/article/39/8/btad525/7251028?login=true