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.
Highlights
Synthetic biology combines ideas from biology and engineering and has the goal of designing and building novel, useful biological systems
We describe the Synthetic Biology Open Language (SBOL) Stack, a platform to allow synthetic biology designs that have been represented in SBOL version 1 or SBOL version 2 to be computationally stored, retrieved, exchanged, and published
The SBOL Stack, which is a database for storing SBOL version 2 in a decomposed Resource Description Framework (RDF) format, where the individual data components are amenable to integration with other data sets
Summary
Synthetic biology combines ideas from biology and engineering and has the goal of designing and building novel, useful biological systems. The promoter is represented with an SBOL ComponentDefinition entity and its role is set to the promoter term from the Sequence Ontology.[12] This entity is associated with a Sequence entity in order to capture the nucleotide sequence of the promoter This graph representation is ideal to execute complex queries using languages designed for navigating RDF graphs, such as SPARQL Protocol and RDF Query Language (SPARQL).[13] Using SPARQL with SBOL RDF enables the expression of complex queries, such as searching for all regulatory interactions for a given coding site or searching for a particular feature among multiple parts. Given the rich promise of functionality afforded by the representation of SBOL in RDF form, there is an overarching need to provide a system that will allow SBOL version 2 to be stored, shared, and queried
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