NP-MRD: Natural Products Magnetic Resonance Database

NP-MRD：天然产物磁共振数据库

• 批准号: 10655369
• 负责人: JOHN R CORT
• 金额: $ 81.51万
• 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/10655369
• 关键词: Acceleration; 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; Ensure; FAIR principles; Frequencies; Gene Cluster; Goals; Harvest; Health; Hour; Human; Humanities; 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; Plants; Policies; Printing; 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; cloud based; community engagement; computing resources; data archive; data exchange; data format; data integrity; data quality/integrity; data repository; data sharing; data submission; density; design; digital object identifier; expectation; experimental study; fungus; heuristics; improved; interactive tool; interoperability; marine organism; metabolome; metabolomics; novel; open data; open source; outreach; public database; quantum; query tools; repository; 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 该项目将开发自然产品磁共振数据库（NP-MRD），中央存储库 对于天然产品社区生成的所有NMR数据。 NP-MRD的核心将是一个开放式访问， 以网络为基础的，以社区为中心的，公平的数据库，其中包含所有人的NMR光谱和结构 已知的天然产物（估计约为350,000个结构）。它将包含（i）遗产（策展人 - 填充）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 由存款人提交的新NP和（iii）启发式计算的所有NP的NMR化学位移， 最终，密度功能理论（DFT）计算了所有NP的化学移位。数据存款都会很快 （<5分钟）和简单。 NP-MRD将与（通过数据交换协议）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），以确保提交的分配数据质量最高。验证和 分析摘要报告将在数据沉积之后提供。 NP-MRD也将提供强大的 数据库搜索，过滤和查询工具，以促进光谱，结构和分类搜索或 选择。除了数据存储，检索和策展外，NP-MRD还将举办大量软件套件 NP研究的工具。这些将包括用于频谱删除，结构验证和基于NMR的工具 复杂混合物的分析。 NP-MRD还将为光谱和结构可视化和 比较，以及化学空间网络可视化和化学征税的比较。此外 NP-MRD将提供用于NMR光谱预测和仿真的工具。 NP-MRD的核心原则是 高质量，增值报告和交互式工具的可用性将鼓励用户参与和数据 沉积。由NP-MRD生产和托管的软件将是开源和开放访问。增强 互操作性，NP-MRD的部分和关联的软件将在云计算上“停靠” 资源，如果需要，将转换为基于Web的API。 NP-MRD的沉积工具将设计为 使用参与期刊的纸质提交软件。 NP-MRD团队将吸引思想领导者， 期刊编辑和数据库经理开发有关数据沉积，数据格式的共识协议 标准和数据交换 - 都符合社区建立的政策和标准。我们的建议 正如主要利益相关者的许多强有力支持信所表明的那样，工作已经获得了吸引力。 NP- MRD将在线和现场（会议上）使用其软件进行NP删除和 鉴别。 NMR光谱和NMR软件中涵盖技巧，技巧和技术的资源将是 通过NP-MRD网站和基于网络的“办公时间”提供可用来帮助用户，存款人和 NP一般社区。 NP-MRD的长期目标是通过 归档并为天然产品NMR数据增加实际价值。

项目成果

NP-MRD: the Natural Products Magnetic Resonance Database.

• DOI: 10.1093/nar/gkab1052
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Wishart DS;Sayeeda Z;Budinski Z;Guo A;Lee BL;Berjanskii M;Rout M;Peters H;Dizon R;Mah R;Torres-Calzada C;Hiebert-Giesbrecht M;Varshavi D;Varshavi D;Oler E;Allen D;Cao X;Gautam V;Maras A;Poynton EF;Tavangar P;Yang V;van Santen JA;Ghosh R;Sarma S;Knutson E;Sullivan V;Jystad AM;Renslow R;Sumner LW;Linington RG;Cort JR
• 通讯作者: Cort JR

A Data Deposition Platform for Sharing Nuclear Magnetic Resonance Data.

共享核磁共振数据的数据沉积平台。

• DOI: 10.1021/acs.jnatprod.3c00795
• 发表时间: 2023
• 期刊: Journal of natural products
• 影响因子: 5.1
• 作者: Pin,Matthew;Poynton,EllaF;Jordan,Tamara;Kim,Jonghyeok;Ledingham,Benjamin;vanSanten,JeffreyA;Yang,Vera;Maras,Andrew;Tavangar,Pegah;Gautam,Vasuk;Peters,Harrison;Sajed,Tanvir;Lee,BrianL;Shreffler,HaileyA;Koller,JamesT;Tret
• 通讯作者: Tret

Microbial natural product databases: moving forward in the multi-omics era.

• DOI: 10.1039/d0np00053a
• 发表时间: 2021-01-01
• 期刊: Natural product reports
• 影响因子: 11.9
• 作者: van Santen JA;Kautsar SA;Medema MH;Linington RG
• 通讯作者: Linington RG