生物元件库国内外研究进展

Research progress of biopart databases

摘要:

生物元件库是对元件数据和实物进行收集、整理和共享的重要平台，对合成生物学的研究和应用具有非常重要的支撑作用。本文对国内外生物元件库的研究进展进行了介绍和综述。国外先后出现了标准生物元件登记库等多个元件库，通过制定OpenMTA协议实现了元件实物的免费分发共享，并通过制定“合成生物学开放语言”（SBOL）实现了多个元件库之间的数据交换；通过bionet项目对元件数据和实物的去中心化管理作了进一步尝试。近年来我们与国内多家科研单位合作建设了合成生物学元件与数据库（RDBSB，https：//www.biosino.org/rdbsb/or https：//www.biosino.org/npbiosys/）。在建设过程中，我们首先建立了与SBOL语言兼容的《催化元件数据标准》、多种重要元件的标准功能测试方法以及安全高效的元件提交系统，并在此基础上完成了元件数量最多且信息最为全面的催化元件数据库的构建。目前，收集了30多万个催化元件，包括7万多个具有文献支持功能表征信息的催化元件，并保藏了1万个以上的实物元件和5000个底盘菌株，通过网站实现了数据和实物的公开与共享。上述元件库已经对国内合成生物学的研究和应用产生了积极地推动作用，访问量超过100万次/年，提供元件和底盘共享服务大于100次/年，并为多家企业和研究单位提供了元件和底盘的定制服务。虽然我们的元件库建设取得了巨大的进步，但是仍需在调控元件的收集整理和共享机制创新等方面取得更多的突破，在数据有源、多层审核、资源共享、信息公开、信息安全和授权访问的基础上，加速生物元件数据、实物和设计工具的汇聚，并进一步服务合成生物学研究。

Abstract:

Biopart databases are the key platforms to collect, sort and share data and physical bioparts, which may promote the research and application of synthetic biology. The research progress of building of biopart database is summarized in this review. There are several databases or registries of bioparts appeared abroad, such as Registry of Standard Biological Parts. In these databases, OpenMTA has been applied to share and distribute bioparts freely; besides, "Synthetic Biology Open Language, SBOL" was developed to exchange the biopart data among different databases; recently a project named as ‘bionet’ has been put on progress to manage, metadata and physical objects of bioparts by decentralized way. We have recently established a biopart database called "Registry and database of bioparts for synthetic biology (RDBSB)" (RDBSB, https://www.biosino.org/rdbsb/or https://www.biosino.org/npbiosys/) by working together with other research institutes. This biopart dabase has been established based on a "data standard for catalytic bioparts" system compatible with SBOL language, and a series of developed standard functional test methods for different sorts of bioparts as well as a set up safe and efficient submission system for bioparts. Until now, RDBSB has collected more than 300000 catalytic bioparts, of which more than 70000 ones have been described with their functional characterization supported by Scientific literatures preserved more than 10000 physical bioparts and 5000 chassis strains, and set up an efficient sharing system to distribute the data and physical bioparts through its website. In the past two years, RDBSB has attracted one million visits per year, and provided more than 100 Services per year to build customized bioparts or chassis strains to researchers or the customized bio-technologic services of build bioparts or chassis for companies and scientific research units per year, which demonstrated its facilitation in the research and application of synthetic biology. However, more breakthroughs are still required in the collection and investigation of regulatory bioparts and innovation of mechanisms for sharing data, metadata physical bioparts and related tools. We are looking forward to building a database with convergence of data, metadata physical objects and design tools to better serve the synthetic biology research basing on a basic regulation including biopart data sourcing, multi-layer reviewing, resource sharing, biopart data disclosure, secured biopart data and authorized access.