NP-MRD: Natural Products Magnetic Resonance Database

NP-MRD：天然产物磁共振数据库

• 批准号: 10434817
• 负责人: JOHN R CORT
• 金额: $ 82.85万
• 依托单位: BATTELLE PACIFIC NORTHWEST LABORATORIES
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10434817
• 关键词: Agreement; Animals; Archaea; Archives; Atlases; Bacteria; Chemicals; Classification; Cloud Computing; Communities; Complement; Complex Mixtures; Computer software; Consensus; Crude Extracts; Data; Data Storage and Retrieval; Databases; Deposition; Disease; Education and Outreach; Ensure; FAIR principles; Frequencies; Gene Cluster; Goals; Gold; Harvest; Health; Hour; Human; Image; Individual; Intuition; Journals; Learning; Letters; Link; Literature; Magnetic Resonance; Mass Spectrum Analysis; Media Campaign; Metadata; Methods; Mining; Molecular; NMR Spectroscopy; National Center for Complementary and Integrative Health; Natural Products; Newsletter; Nuclear Magnetic Resonance; Online Systems; Paper; Policies; Privatization; Process; Protocols documentation; Publications; Reporting; Research; Resolution; Resources; Retrieval; Running; Scientific Societies; Scientist; Sister; Site; Social Network; Software Tools; Source; Structure; Summary Reports; Taxonomy; Techniques; Text; Time; Traction; Training; Translations; Validation; Vendor; Visualization; Visualization software; Work; base; cloud based; community engagement; computing resources; data archive; data exchange; data format; data integrity; data quality; data repository; data sharing; data submission; density; design; digital object identifier; expectation; experimental study; heuristics; improved; interactive tool; interoperability; marine organism; metabolome; metabolomics; novel; open data; open source; plant fungi; public database; quantum; query tools; repository; searchable database; simulation; social; social media; symposium; theories; tool; user-friendly; web site; web-enabled; webinar

PROJECT SUMMARY This project will develop the Natural Products Magnetic Resonance Database (NP-MRD), the central repository for all NMR data generated by the natural products community. The core of the NP-MRD will be an open-access, web-enabled, community-focused, FAIR-compliant database containing NMR spectra and structures for all known natural products (estimated to be ~350,000 structures). It will contain (i) legacy (curator-backfilled) NMR data of NPs derived from the literature, existing public databases, and “private” data archives, (ii) new NMR data submitted by depositors for novel NPs, and (iii) heuristically calculated NMR chemical shifts for all NPs and, eventually, density functional theory (DFT) calculated chemical shifts all NPs. Data deposition will be both rapid (<5 minutes) and simple. The NP-MRD will be closely integrated (through data exchange agreements) with “sister” databases containing MS, biosynthetic gene cluster, and bioactivity data. It will provide rigorous validation and data checking (QA/QC) to ensure that submitted assignment data is of the highest quality. Validation and analytical summary reports will be provided following data deposition. The NP-MRD will also offer powerful database search, filtering, and querying tools to facilitate spectral, structure and taxonomic searches or selections. In addition to data storage, retrieval, and curation, the NP-MRD will host an extensive suite of software tools for NP research. These will include tools for spectral dereplication, structure validation, and NMR-based profiling of complex mixtures. The NP-MRD will also provide tools for spectral and structural visualization and comparison, as well as chemical-space network visualization and chemo-taxonomic comparisons. Additionally the NP-MRD will offer tools for NMR spectral prediction and simulation. A core principle of the NP-MRD is that availability of high-quality, value-added reporting and interactive tools will encourage user engagement and data deposition. Software produced and hosted by the NP-MRD will be open-source and open-access. To enhance interoperability, portions of the NP-MRD and associated software will be “dockerized” on cloud computing resources and, if needed, converted to web-based APIs. The NP-MRD’s deposition tools will be designed to work with participating journals’ paper-submission software. The NP-MRD team will engage thought leaders, journal editors, and database managers to develop consensus protocols regarding data deposition, data format standards, and data exchange—all compliant with community-established policies and standards. Our proposed work has already gained traction, as shown by many strong letters of support from key stakeholders. The NP- MRD will offer online and on-site (at conferences) training on use of its software for NP dereplication and identification. Resources covering tips, tricks, and techniques in NMR spectroscopy and NMR software will be made available on the NP-MRD website and through web-based “office hours” to help users, depositors, and the general NP community. NP-MRD’s long-term goal is to advance and enable natural products research by archiving and adding real value to natural product NMR data.

项目摘要 该项目将开发天然产物磁共振数据库（NP-MRD）， 天然产物社区生成的所有NMR数据。NP-MRD的核心是开放获取， 一个网络化的、以社区为中心的、符合FAIR标准的数据库，包含所有人的NMR光谱和结构。 已知的天然产物（估计约有350，000种结构）。它将包含（i）遗留（管理员回填）NMR 来自文献、现有公共数据库和“私人”数据档案的NP数据，（ii）新的NMR数据 由新NP的保藏者提交，和（iii）所有NP的图解计算的NMR化学位移，和， 最后，用密度泛函理论（DFT）计算了所有NP的化学位移。数据存储将迅速 （5分钟）简单。国家方案监测和报告司将（通过数据交换协定）与 包含MS、生物合成基因簇和生物活性数据的“姐妹”数据库。它将提供严格的验证 和数据检查（QA/QC），以确保提交的作业数据具有最高质量。验证和 分析摘要报告将在数据存放后提供。NP-MRD还将提供强大的 数据库搜索、过滤和查询工具，以促进光谱、结构和分类学搜索，或 选择。除了数据存储、检索和管理之外，NP-MRD还将托管一套广泛的软件 NP研究的工具。这些将包括用于光谱去复制、结构验证和基于NMR的分析的工具。 复杂混合物的分析。NP-MRD还将提供光谱和结构可视化工具， 比较，以及化学空间网络可视化和化学分类比较。另外 NP-MRD将为NMR谱预测和模拟提供工具。NP-MRD的核心原则是， 提供高质量、增值的报告和互动工具将鼓励用户参与， 证词NP-MRD制作和托管的软件将是开源和开放获取的。加强 互操作性，部分NP-MRD和相关软件将在云计算上“对接” 资源，并在需要时转换为基于Web的API。NP-MRD的沉积工具将被设计为 使用参与期刊的论文提交软件。NP-MRD团队将邀请思想领袖， 期刊编辑和数据库管理员，以制定关于数据存放、数据格式 标准和数据交换-所有这些都符合社区制定的政策和标准。我们提出的 正如主要利益攸关方发出的许多强有力的支持信所表明的那样，这项工作已经取得了进展。NP- 监测和研究司将提供在线和现场（在会议上）培训，内容是如何使用其软件进行国家处理程序的复制删除， 识别.资源涵盖的提示，技巧，并在NMR光谱和NMR软件技术将 通过NP-MRD网站和基于网络的“办公时间”提供，以帮助用户，存款人， NP社区。NP-MRD的长期目标是通过以下方式推进和实现天然产品研究： 对天然产物NMR数据进行存档并增加真实的价值。