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Curation Principles Derived from the Analysis of the SBOL iGEM Data Set
ACS Synthetic Biology ( IF 3.7 ) Pub Date : 2021-09-21 , DOI: 10.1021/acssynbio.1c00225
Jeanet Mante 1 , Nicholas Roehner 2 , Kevin Keating 3 , James Alastair McLaughlin 4 , Eric Young 3 , Jacob Beal 2 , Chris J Myers 1
Affiliation  

As an engineering endeavor, synthetic biology requires effective sharing of genetic design information that can be reused in the construction of new designs. While there are a number of large community repositories of design information, curation of this information has been limited. This in turn limits the ways in which design information can be put to use. The aim of this work was to improve this situation by creating a curated library of parts from the International Genetically Engineered Machines (iGEM) registry data set. To this end, an analysis of the Synthetic Biology Open Language (SBOL) version of the iGEM registry was carried out using four different approaches—simple statistics, SnapGene autoannotation, SYNBICT autoannotation, and expert analysis—the results of which are presented herein. Key challenges encountered include the use of free text, insufficient part provenance, part duplication, lack of part removal, and insufficient continuous curation. On the basis of these analyses, the focus has shifted from the creation of a curated iGEM part library to instead the extraction of a set of lessons, which are presented here. These lessons can be exploited to facilitate the creation and curation of other part libraries using a simpler and less labor intensive process.

中文翻译:

源自对 SBOL iGEM 数据集的分析的策展原则

作为一项工程努力,合成生物学需要有效共享基因设计信息,这些信息可以在新设计的构建中重复使用。虽然有许多设计信息的大型社区存储库,但对这些信息的管理是有限的。这反过来又限制了设计信息的使用方式。这项工作的目的是通过从国际基因工程机器(iGEM) 注册数据集中创建一个精选的零件库来改善这种情况。为此,对合成生物学开放语言进行了分析(SBOL) 版本的 iGEM 注册表是使用四种不同的方法进行的——简单统计、SnapGene 自动注释、SYNBICT 自动注释和专家分析——其结果在本文中介绍。遇到的主要挑战包括使用自由文本、部分出处不足、部分重复、部分删除不足和持续管理不足。在这些分析的基础上,重点已从创建精选的 iGEM 零件库转移到提取一组课程,此处介绍。可以利用这些经验教训使用更简单且劳动强度较低的过程来促进其他零件库的创建和管理。
更新日期:2021-10-15
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