The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery
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DOI：
10.1021/acscentsci.9b00806
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发表时间：
2019-11-27
影响因子：
18.2
通讯作者：
Linington, Roger G.
中科院分区：
文献类型：
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作者：
van Santen, Jeffrey A.;Jacob, Gregoire;Linington, Roger G.
尽管微生物天然产物化学领域发展迅速，但目前还没有包含所有微生物生产的天然产物结构的开放获取数据库。这些数据的缺乏阻碍了天然产品科学新技术的实施。具体地说，由于缺乏用于比较实验数据的已知化合物的全面数据库，新的化合物表征和鉴定计算策略的开发正受到阻碍。建立一个开放获取、由社区维护的微生物天然产品结构数据库将有助于开发天然产品发现方面的新技术，并改善现有天然产品数据资源的互操作性。然而，这些数据在历史科学文献中分布不均，包括期刊文章和国际专利。这些文件没有标准格式，通常不作为机器可读文本数字化，也不公开提供。此外，这些文档中没有一个具有相关联的结构文件(例如，MOL、INCHI或SILES)，而是包含结构的图像。这使得相关天然产品数据的提取和格式化成为一项艰巨的挑战。使用人工管理和自动数据挖掘相结合的方法，我们创建了一个微生物天然产品数据库(天然产品图集，www.npatlas.org)，其中包括24594种化合物，并包含结构、化合物名称、来源生物、分离参考、全合成和结构重新分配实例的参考数据。该数据库配有一个交互式门户网站，允许按结构、子结构和物理属性进行搜索。该网站还提供了将自然产品、化学空间和仪表板可视化的机制，以显示作者和发现时间表数据。这些交互式工具为天然产品发现提供了强大的知识库，并提供了基于结构和属性的搜索的中央界面，并提出了关于天然产品结构多样性的新观点。天然产品图谱是根据公平原则(可查找、可访问、可互操作和可重复使用)开发的，并与其他新兴的天然产品数据库相结合，包括关于生物合成基因群(MIBiG)储存库的最低信息，以及全球天然产品社会分子网络(GNPS)平台。它被设计为一个社区支持的资源，为来自微生物的已知天然产品结构提供一个中央储存库，是第一个这种类型的全面、开放获取的资源。预期《天然产品图集》将有助于开发新的天然产品发现模式，并加快复杂天然产品库结构特征的确定进程。
Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced natural product structures. Lack of availability of these data is preventing the implementation of new technologies in natural products science. Specifically, development of new computational strategies for compound characterization and identification are being hampered by the lack of a comprehensive database of known compounds against which to compare experimental data. The creation of an open access, community-maintained database of microbial natural product structures would enable the development of new technologies in natural products discovery and improve the interoperability of existing natural products data resources. However, these data are spread unevenly throughout the historical scientific literature, including both journal articles and international patents. These documents have no standard format, are often not digitized as machine readable text, and are not publicly available. Further, none of these documents have associated structure files (e.g., MOL, InChI, or SMILES), instead containing images of structures. This makes extraction and formatting of relevant natural products data a formidable challenge. Using a combination of manual curation and automated data mining approaches we have created a database of microbial natural products (The Natural Products Atlas, www.npatlas.org) that includes 24 594 compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. This database is accompanied by an interactive web portal that permits searching by structure, substructure, and physical properties. The Web site also provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. These interactive tools offer a powerful knowledge base for natural products discovery with a central interface for structure and property-based searching and presents new viewpoints on structural diversity in natural products. The Natural Products Atlas has been developed under FAIR principles (Findable, Accessible, Interoperable, and Reusable) and is integrated with other emerging natural product databases, including the Minimum Information About a Biosynthetic Gene Cluster (MIBiG) repository, and the Global Natural Products Social Molecular Networking (GNPS) platform. It is designed as a community-supported resource to provide a central repository for known natural product structures from microorganisms and is the first comprehensive, open access resource of this type. It is expected that the Natural Products Atlas will enable the development of new natural products discovery modalities and accelerate the process of structural characterization for complex natural products libraries.