NP-MRD: Natural Products Magnetic Resonance Database

NP-MRD：天然产物磁共振数据库

基本信息

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
项目类别：
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

项目摘要

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。