The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

Wipat, A; Hallinan, J; Madsen, C; McLaughlin, JA; Mısırlı, G; Pocock, M; Flanagan, K

Abstract

Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.

Citation

Wipat, A., Hallinan, J., Madsen, C., McLaughlin, J., Mısırlı, G., Pocock, M., & Flanagan, K. (2016). The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs. ACS synthetic biology, 487 - 497. https://doi.org/10.1021/acssynbio.5b00210

• Acceptance Date: Oct 21, 2015
• Publication Date: Jun 7, 2016
• Journal: ACS Synthetic Biology
• Publisher: American Chemical Society
• Pages: 487 - 497
• DOI: https://doi.org/10.1021/acssynbio.5b00210
• Keywords: data standards; database; RDF: synthetic biology; Synthetic Biology Open Language (SBOL); triplestore
• Publisher URL: http://pubs.acs.org/doi/abs/10.1021/acssynbio.5b00210