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.

项目摘要 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 平台建立在一组已建立的组件上，包括Terra Computing平台和Dockstore 用于基于标准的集装箱工具和工作流程。它还为 数据访问和分析，包括带有Terra的批处理工作流程，笔记本电脑环境，包括Jupyter和 rstudio，用于砧座API和服务顶部建筑物分析的生物通用套件，并将很快提供 银河系实例进行互动分析。通过为数据管理提供统一的环境， 计算，铁砧消除了对数据移动的需求，可以控制访问敏感数据和 监视并提供可根据需要的研究人员获得的弹性，共享的计算资源。 NIH赞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建立了主要的云门户网站，First，Topmed，TCGA和其他几项主要举措。 但是，一起使用这些系统是一个挑战。个别数据门户使研究人员能够浏览 并查询自己的数据，但功能有限，可以在门户上共享数据或用户注册或 具有基于云的工作区，例如Terra和Galaxy。最近建立的NIH云平台 互操作性（NCPI）的工作旨在通过实施关键的互操作技术来解决这些问题 跨多个NIH机构。在这个项目下，我们将在NCPI工作组中工作以定义使用 互操作性的案例和标准，并实施三种主要技术 砧座的NCPI和r/bioconductor成分。首先，我们将实施NIH 研究人员授课服务（RAS）为研究人员提供了一种共同的机制，以建立其身份和 访问数据被授权在Terra和Galaxy上使用。其次，我们将实施全球联盟 用于基因组学和健康（GA4GH）数据存储库服务（DRS），以便数据消费者（包括 工作流系统，无论存储在哪里，都可以以单一的标准方式访问数据对象 它们的管理方式。最后，我们将在Anvil中为快速医疗保健提供初步支持 互操作资源（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），特别是为了确保这些记录可用，可发现和 可以理解的是，患者围绕医疗保健生态系统移动。砧座的FHIR支持将有助于 一旦数据摄入砧，用户就可以访问Emerge和相关项目。