Zieliński Tomasz, Hay Johnny, Romanowski Andrew, Nenninger Anja, McCormick Alistair, Millar Andrew J
SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
EPCC, University of Edinburgh, Edinburgh, UK.
Synth Biol (Oxf). 2022 Jan 26;7(1):ysac002. doi: 10.1093/synbio/ysac002. eCollection 2021.
Practical delivery of Findable, Accessible, Reusable and Interoperable principles for research data management requires expertise, time resource, (meta)data standards and formats, software tools and public repositories. The Synthetic Biology Open Language (SBOL2) metadata standard enables FAIR sharing of the designs of synthetic biology constructs, notably in the repository of the SynBioHub platform. Large libraries of such constructs are increasingly easy to produce in practice, for example, in DNA foundries. However, manual curation of the equivalent libraries of designs remains cumbersome for a typical lab researcher, creating a barrier to data sharing. Here, we present a simple tool SynBio2Easy, which streamlines and automates operations on multiple Synthetic Biology Open Language (SBOL) designs using tables as metadata inputs. The tool provides several utilities for manipulation of SBOL documents and interaction with SynBioHub: for example, generation of a library of plasmids based on an original design template, bulk deposition into SynBioHub, or annotation of existing SBOL component definitions with notes and authorship information. The tool was used to generate and deposit a collection of 3661 cyanobacterium plasmids into the public SynBioHub repository. In the process of developing the software and uploading these data, we evaluated some aspects of the SynBioHub platform and SBOL ecosystem, and we discuss proposals for improvement that could benefit the user community. With software such as SynBio2Easy, we aim to deliver a user-driven tooling to make FAIR a reality at all stages of the project lifecycle in synthetic biology research. Graphical Abstract.
为研究数据管理切实实现可查找、可访问、可重用和可互操作原则，需要专业知识、时间资源、（元）数据标准和格式、软件工具以及公共存储库。合成生物学开放语言（SBOL2）元数据标准能够实现合成生物学构建体设计的公平共享，尤其是在SynBioHub平台的存储库中。实际上，越来越容易在例如DNA铸造厂中生产大量此类构建体库。然而，对于典型的实验室研究人员而言，手动整理等效的设计库仍然很繁琐，这为数据共享造成了障碍。在此，我们展示了一个简单的工具SynBio2Easy，它使用表格作为元数据输入，简化并自动化了对多个合成生物学开放语言（SBOL）设计的操作。该工具提供了多种用于操作SBOL文档以及与SynBioHub交互的实用程序：例如，基于原始设计模板生成质粒库、批量存入SynBioHub，或使用注释和作者信息对现有SBOL组件定义进行注释。该工具用于生成3661个蓝细菌质粒的集合并将其存入公共的SynBioHub存储库。在开发软件和上传这些数据的过程中，我们评估了SynBioHub平台和SBOL生态系统的一些方面，并讨论了可能使用户群体受益的改进建议。借助诸如SynBio2Easy之类的软件，我们旨在提供一种用户驱动的工具，以使合成生物学研究项目生命周期的各个阶段都能实现公平原则。图形摘要。
