Research progress of biopart databases

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.