Implementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

实施基因组数据科学分析、可视化和信息学实验室空间 (AnVIL)

• 批准号: 10220581
• 负责人: Jeremy Goecks
• 金额: $ 40万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-21 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10220581
• 关键词: Address; Bioconductor; Biomedical Research; Data; Data Analyses; Data Science; Data Storage and Retrieval; Ecosystem; Electronic Health Record; Elements; Ensure; Environment; Fast Healthcare Interoperability Resources; Galaxy; Genomics; Genotype-Tissue Expression Project; Healthcare; Individual; Informatics; Institutes; Monitor; Movement; National Human Genome Research Institute; Patients; Records; Research; Research Personnel; Services; System; Systems Analysis; Technology; The Cancer Genome Atlas; Trans-Omics for Precision Medicine; United States National Institutes of Health; Visualization; Work; base; cloud based; cloud platform; computational platform; computing resources; data access; data format; data ingestion; data management; data portal; data resource; data sharing; data warehouse; genomic data; health data; interoperability; molecular phenotype; next generation; phenotypic data; tool; working group

Project Summary The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) powers the next generation of computational genomics research using cloud-scale data and compute resources. The platform is built on a set of established components, including the Terra computing platform and Dockstore for standards-based sharing of containerized tools and workflows. It also provides multiple entry points for data access and analysis, including batch workflows with Terra, notebook environments including Jupyter and RStudio, Bioconductor packages for building analysis on top of AnVIL APIs and services, and will soon offer Galaxy instances for interactive analysis. By providing a unified environment for data management and compute, AnVIL eliminates the need for data movement, allows for controlled access to sensitive data and monitoring, and provides elastic, shared computing resources that can be acquired by researchers as needed. NIH-sponsored biomedical research is increasingly moving to cloud-based data storage and analysis systems, with major cloud portals established for GTEx, Kids First, TOPMed, TCGA and several other major initiatives. However, using these systems together is a challenge. The individual data portals enable researchers to browse and query their own data but have limited functionality to share data or user registrations across portals or with cloud based workspaces, like Terra and Galaxy. The recently established NIH Cloud Platform Interoperability (NCPI) effort aims to address these issues by implementing key interoperability technologies across multiple NIH institutes. Under this project, we will work the NCPI working groups to define the use cases and standards for interoperability as well as implement three major technologies recommended by the NCPI within the Galaxy and R/Bioconductor components of AnVIL. First, we will implement the NIH Researcher Auth Service (RAS) to provide a common mechanism for researchers to establish their identity and access data they are authorized to use across Terra and Galaxy. Second, we will implement the Global Alliance for Genomics and Health (GA4GH) Data Repository Service (DRS) so that data consumers, including workflow systems, can access data objects in a single, standard way regardless of where they are stored and how they are managed. Finally, we will develop initial support in AnVIL for the Fast Healthcare Interoperability Resources (FHIR) standard. This standard describes data formats, elements, and an API for exchanging electronic health records (EHR), especially to ensure these records are available, discoverable, and understandable as patients move around the healthcare ecosystem. FHIR support in AnVIL will facilitate access to eMERGE and related projects by users once the data are ingested in AnVIL.

项目概要 NHGRI 基因组数据科学分析、可视化和信息学实验室空间 (AnVIL) 为 使用云规模数据和计算资源的下一代计算基因组学研究。这 平台构建在一组已建立的组件之上，包括 Terra 计算平台和 Dockstore 用于基于标准的容器化工具和工作流程共享。它还提供了多个入口点 数据访问和分析，包括 Terra 的批处理工作流程、笔记本环境（包括 Jupyter 和 RStudio，Bioconductor 软件包，用于在 AnVIL API 和服务之上构建分析，并将很快提供 用于交互式分析的 Galaxy 实例。通过提供统一的数据管理环境 计算，AnVIL 消除了数据移动的需要，允许对敏感数据进行受控访问，并且 监控，并提供研究人员可以根据需要获取的弹性、共享计算资源。 NIH 资助的生物医学研究越来越多地转向基于云的数据存储和分析系统， 为 GTEx、Kids First、TOPMed、TCGA 和其他几个主要计划建立了主要的云门户。 然而，同时使用这些系统是一个挑战。各个数据门户使研究人员能够浏览 并查询自己的数据，但跨门户共享数据或用户注册的功能有限，或者 具有基于云的工作空间，例如 Terra 和 Galaxy。最近建立的NIH云平台 互操作性 (NCPI) 工作旨在通过实施关键的互操作性技术来解决这些问题 跨越多个 NIH 机构。在这个项目下，我们将与 NCPI 工作组合作来定义使用 互操作性的案例和标准以及实施委员会推荐的三项主要技术 Galaxy 内的 NCPI 和 AnVIL 的 R/Bioconductor 组件。首先，我们将实施 NIH 研究人员身份验证服务 (RAS) 为研究人员提供一种通用机制来建立其身份和信息 访问他们被授权在 Terra 和 Galaxy 中使用的数据。第二，我们将实施全球联盟 基因组学和健康 (GA4GH) 数据存储服务 (DRS)，以便数据消费者，包括 工作流系统可以以单一、标准的方式访问数据对象，无论它们存储在何处 如何管理它们。最后，我们将在 AnVIL 中为 Fast Healthcare 提供初步支持 互操作性资源 (FHIR) 标准。该标准描述了数据格式、元素和 API 交换电子健康记录 (EHR)，特别是确保这些记录可用、可发现和 当患者在医疗保健生态系统中移动时，这是可以理解的。 AnVIL 中的 FHIR 支持将促进 一旦数据被摄取到 AnVIL 中，用户就可以访问 eMERGE 和相关项目。