Data Management and Bioinformatics Core

数据管理和生物信息学核心

• 批准号: 10551463
• 负责人: JUSTIN B. STARREN
• 金额: $ 28.3万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-17 至 2027-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10551463
• 关键词: Acceleration; Address; Alveolar; Area; Awareness; Bioinformatics; Biological; Biological Models; Clinical; Clinical Data; Code; Complex; Cytometry; Data; Data Set; Data Sources; Dependence; Ensure; Equilibrium; Foundations; Frequencies; Future; Generations; Genome; Goals; Hospitals; Human; Informatics; Infrastructure; Ingestion; Knowledge; Machine Learning; Medical; Metadata; Methods; Modeling; Multiomic Data; Names; Nature; Outcome; Participant; Pathology; Patients; Persons; Phase; Plant Leaves; Play; Pneumonia; Preparation; Privacy; Process; Property; Reproducibility; Research; Research Personnel; Resources; Sampling; Science; Secure; Security; Specimen; System; Systems Biology; Techniques; Time; Weight; advanced system; cohort; community acquired pneumonia; computer infrastructure; computerized tools; computing resources; data infrastructure; data management; data modeling; data quality; data sharing; design; diverse data; empowerment; experience; health data; heterogenous data; high dimensionality; improved; innovation; insight; multidimensional data; multidisciplinary; novel; open source; pathogen; patient subsets; phenome; pneumonia treatment; query tools; recurrent neural network; response; skills; success; tool; treatment response; ventilator-associated pneumonia

Project Summary/Abstract – Data Management and Bioinformatics Core This innovative integrated systems biology application seeks to further delineate the complex host/pathogen interactions occurring at the alveolar level that lead to unsuccessful response to therapy in serious pneumonia. The SCRIPT2 Systems Biology Center is intentionally multidisciplinary, increasing the complexity of interactions and mandating a centralized approach to facilitate accomplishing the goals of this Systems Biology Center. The overall goal of the Data Management and Bioinformatics (DMBI) Core is to develop and implement new and enhanced computational resources that support SCRIPT2, and to share those resources broadly. The DMBI Core will sit at the nexus of SCRIPT2 where it will provide the tools, methods, skills and infrastructure to collect, integrate, transform, analyze and distribute the diverse data generated by the projects. The design and implementation of the DMBI Core is based on the premise that genome-centric approaches and phenome- centric approaches are both inherently scientifically limiting. Rather, a systems biology approach that gives equal weight to all data types is more likely to produce significant findings. For the first phase of SCRIPT, the DMBI Core developed a rich data infrastructure to support the integrative analysis of clinical and multi-omic data. We will build on this foundation for SCRIPT2. The DMBI Core will advance systems biology data management in three areas. First, expanding beyond existing processes for data quality assessment, automated real-time flagging of anomalies based on statistical properties of past data, external data, and public knowledge will guide subsequent inspection toward technical rigor, biological novelty, the identification of rare patient subgroups, and provide near-time identification of emerging changes in the pathologies present by recent patients. Second, we will extend our existing SCRIPT infrastructure to allow rapid cohort identification, hypothesis generation, and analytic dataset creation. We propose extending the open-source Leaf query tool to perform both person-based and sample-based queries against both the Observational Medical Outcomes Partnership (OMOP) common data model and study-specific datasets. Tracking of specimens through the various stages of experimental and computational processing – and providing estimates of future data availability – will assist project management and preparations toward future data usage and modeling. Third, the combination of clinical data with multi-omic data with newer computational tools that combine code and data creates unique data and security challenges. Expanding on our experiences in SCRIPT to raise awareness of best practices for securely using and sharing data and models while ensuring privacy, in SCRIPT2 we will streamline processes and develop novel tools and methods to ensure a rapid and fair balance between privacy and data utility.

项目摘要/摘要-数据管理和生物信息学核心 这种创新的综合系统生物学应用旨在进一步描绘复杂的宿主/病原体 在肺泡水平发生的相互作用导致严重肺炎治疗无效。 该中心是多学科的，增加了相互作用的复杂性 并授权一个集中的方法，以促进实现这个系统生物学中心的目标。 数据管理和生物信息学（DMBI）核心的总体目标是开发和实施新的 以及支持WITT 2的增强型计算资源，并广泛共享这些资源。的 DMBI核心将位于CUT 2的核心，它将提供工具、方法、技能和基础设施， 收集、整合、转换、分析和分发项目产生的各种数据。设计 和DMBI核心的实施是基于这样的前提，即以基因组为中心的方法和表型- 以中心为中心的方法都具有内在的科学局限性。相反，一种系统生物学方法， 对所有数据类型给予同等权重更有可能产生重要的调查结果。在第一阶段， DMBI Core开发了丰富的数据基础设施，以支持临床和多组学的综合分析 数据我们将在此基础上为2012年奠定基础。DMBI核心将推进系统生物学数据 三个方面的管理。首先，扩展现有的数据质量评估程序， 基于过去数据、外部数据的统计特性自动实时标记异常， 公众知识将指导随后的检查，以技术严谨性，生物新奇， 罕见患者亚组，并提供当前病理学中新出现变化的近时间识别 最近的病人。第二，我们将扩展现有的CIMT基础设施， 识别、假设生成和分析数据集创建。我们建议扩展开源 Leaf查询工具，用于对Observational 医学成果伙伴关系（OMOP）通用数据模型和研究特定数据集。跟踪 标本通过实验和计算处理的各个阶段-并提供 对未来数据可用性的估计-将有助于项目管理和对未来数据的准备 使用和建模。第三，临床数据与多组学数据的结合， 结合联合收割机代码和数据的工具产生了独特的数据和安全挑战。扩大我们的经验 提高对安全使用和共享数据和模型的最佳实践的认识，同时确保 隐私，在2012年，我们将简化流程，开发新的工具和方法，以确保快速， 隐私和数据效用之间的平衡。