NMRbox information management: CONNJUR and BMRB integration

NMRbox 信息管理：CONNJUR 和 BMRB 集成

• 批准号: 10652470
• 负责人: JEFFREY C HOCH
• 金额: $ 38.03万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10652470
• 关键词: Biomolecular Nuclear Magnetic Resonance; Chemicals; Collection; Communities; Complex; Computer software; Consumption; Custom; Data; Data Analyses; Data Set; Deposition; Development; Ensure; Environment; Extensible Markup Language; Fostering; Glean; Goals; Harvest; Individual; Information Management; Investigation; Knowledge; Libraries; Manuals; Metadata; Occupations; Operating System; Pathway interactions; Process; Productivity; Pythons; Recording of previous events; Reporting; Reproducibility; Research; Research Personnel; Resources; Sampling; Services; Software Tools; System; Time; Translations; Validation; Work; analytical tool; cluster computing; computerized data processing; data dictionary; data modeling; data repository; data submission; data visualization; design; experimental study; file format; improved; interoperability; metabolomics; open source; preservation; prototype; public database; reconstruction; repository; small molecule; tool

TRD2 Summary Biomolecular NMR data computation is complex, requiring both semi-automated and manual processing steps. The NMRbox platform provides easy access to the myriad software tools used during an individual investigation. The efforts of TRD1 ensure that all of this software functions within the same operating system environment. The goals of TRD2 are to provide information management solutions to promote software interoperability across the NMRbox platform (TRD1) and with the analytics of TRD3; to foster reproducibility through the active curation of scientific datasets and workflows; to facilitate the integration of experimental and derived data with information from public databases to generate new knowledge, and to help aggregate this diverse panoply of experimental data and metadata to create and facilitate richer depositions to the appropriate public data repositories. A key component to enriching repository depositions is the collection of provenance metadata which reports on the history or lineage of how computations were orchestrated and intermediate and final results obtained. Knowing the pathway of how results were obtained is a critical component to reproducing and building upon scientific claims. The aims of this project period are fourfold. The CONNJUR data model and CONNJUR software integration environments (integral components of NMRbox) will be extended to capture more metadata to support the tracking of provenance (or data lineage), to foster reproducibility, to promote software interoperability both within and without NMRbox, and to support a richer metadata set for depositions to the public data repositories. In addition, the workflow management system will be extended to support high-throughput computational workflows by connecting to powerful job management systems such as HTCondor and DAGMan. The data and process logging capabilities of NMRbox will be used for automatic harvesting of whatever metadata can be gleaned by these mechanisms. Finally, more direct access to BMRB resources will be provided through direct machine-to- machine services.

TRD2总结 生物分子 NMR 数据计算很复杂，需要半自动和手动处理步骤。 NMRbox 平台可以轻松访问个人调查期间使用的各种软件工具。 TRD1 的努力确保所有这些软件都能在同一操作系统环境中运行。 TRD2 的目标是提供信息管理解决方案，以促进跨领域的软件互操作性 NMRbox 平台 (TRD1) 和 TRD3 的分析；通过积极的管理来促进可重复性 科学数据集和工作流程；促进实验数据和派生数据与信息的整合 从公共数据库中生成新知识，并帮助聚合这些多样化的实验 数据和元数据，以创建并促进更丰富的存储到适当的公共数据存储库。一把钥匙 丰富存储库沉积物的组成部分是来源元数据的收集，该元数据报告了 如何编排计算以及获得中间和最终结果的历史或沿袭。会心 如何获得结果的途径是复制和建立科学的关键组成部分 索赔。 该项目期间的目标有四个。 CONNJUR 数据模型和 CONNJUR 软件集成 环境（NMRbox 的集成组件）将得到扩展，以捕获更多元数据来支持 跟踪出处（或数据沿袭），以促进可重复性，促进软件内部的互操作性 无需 NMRbox，并支持更丰富的元数据集以存储到公共数据存储库。在 此外，工作流程管理系统将得到扩展，以支持高通量计算工作流程 通过连接到强大的作业管理系统（例如 HTCondor 和 DAGMan）。数据和过程 NMRbox 的日志记录功能将用于自动收集可以通过以下方式收集的任何元数据： 这些机制。最后，将通过直接机器对 BMRB 资源提供更直接的访问 机服务。