Epstein Samuel C, Charkoudian Louise K, Medema Marnix H
1Department of Chemistry, Haverford College, Haverford, PA 19041-1391 USA.
2Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
Stand Genomic Sci. 2018 Jul 11;13:16. doi: 10.1186/s40793-018-0318-y. eCollection 2018.
Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.
微生物利用复杂的酶促途径来生物合成结构复杂且具有药理学相关性的分子。这些途径由基因簇编码，存在于各种各样的生物体中。生物合成基因簇知识库通过利用用户提交的数据将科学发现转化为可进行计算分析的格式，促进了关于这些基因簇及其分子产物的实验数据的标准化和集中存储。这加速了将基因与化学结构联系起来的过程，在环境多样性的背景下理解生物合成基因簇，以及进行合成基因簇的计算机辅助设计。在此，我们展示了一个标准操作规程、Excel模板、一个教程视频以及一系列相关的综述文献，以支持科学家们将数据提交到生物合成基因簇知识库中。此外，我们提供工具将基因簇注释项目整合到课堂环境中，包括工作流程和评估材料。
