The AnVIL Data Ecosystem

AnVIL 数据生态系统

• 批准号: 10231107
• 负责人: Robert J Carroll
• 金额: $ 450万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-19 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10231107
• 关键词: Address; Advisory Committees; All of Us Research Program; Architecture; Atlases; Catalogs; Cells; Chicago; Cloud Computing; Collaborations; Communities; Computer software; Consultations; Cost Control; Data; Data Engineering; Data Science; Data Set; Documentation; Ecosystem; Educational workshop; Ensure; Environment; Genomic Data Commons; Genotype; Goals; Human; Human Genetics; Institutes; Lead; Licensing; Metadata; Modeling; National Human Genome Research Institute; Phenotype; Play; Research; Research Personnel; Resources; Role; Secure; Security; Services; Software Engineering; Standardization; System; United States National Institutes of Health; Washington; Work; cloud based; community engaged research; community engagement; data access; data ecosystem; data modeling; data resource; data sharing; data standards; data tools; digital; experience; functional genomics; genome sciences; genomic data; indexing; innovation; interoperability; member; novel; novel strategies; open source; operation; phenotypic data; repository; software development; software systems; tool

The AnVIL Data Ecosystem Project Summary / Abstract In this proposal, we bring together a unified team with a strong track record of developing secure and scalable software systems to support flagship scientific efforts, such as the All of Us Research Program, the Genomic Data Commons (GDC), and the Human Cell Atlas (HCA). Our group will leverage these experiences, and the software developed for them, to create an ecosystem of applications that will both serve the needs of the AnVIL and interoperate with other NIH data resources. We will accomplish this through the following Aims: ● Aim 1 (Software Engineering): Leverage existing software capabilities to create tools for storing, sharing, and analyzing AnVIL datasets at unlimited scale. During the past five years, our groups have created a suite of modular and open source software capabilities that address key needs in genomic data science. We will leverage these existing capabilities and extend them in novel directions to address AnVIL-specific scientific goals relating to human genetics and functional genomics. ● Aim 2 (Data Engineering): Curate data and metadata resources so that they are easily accessible. The AnVIL will not only be a suite of software services, but also a vast repository of genotypic and phenotypic information. For this resource to be usable by the community, it must be organized, curated, and made accessible. We will accomplish this by processing genomic datasets using a consistent set of best-practices pipelines, and mapping phenotypes to a common data model. ● Aim 3 (Operations): Stand up and support a data environment for the AnVIL community, and integrate it with other NIH resources as part of a federated NIH-wide genomic data commons. The modular components of Aim 1 are critical building blocks, but they alone are not enough to meet the needs of the AnVIL; they must also be stood up as services and integrated into a coherent entity, which we call a “data environment.” We propose to create an AnVIL data environment that will enable researchers to access datasets in a secure, compliant, and facile manner. The guiding principle of these efforts is that progress in genomic science will happen most rapidly if there is a diversity of solutions created by a plurality of groups. Towards that end, our approach to engineering the software components of Aim 1, curating the datasets of Aim 2, and operating the software services of Aim 3 is to catalyze an ecosystem of activity around the AnVIL. Our proposal focuses not only on creating and operating software services ourselves, but also on incorporating third-party solutions. We propose to accomplish this by architecting the AnVIL data environment according to the following principles: (i) modularity, (ii) openness, (iii) community engagement, (iv) standardization, and (v) interoperability.

AnVIL 数据生态系统 项目概要/摘要 在此提案中，我们汇集了一个统一的团队，该团队在开发安全和可扩展性方面拥有良好的记录 支持旗舰科学工作的软件系统，例如“我们所有人研究计划”、“基因组计划” 数据共享 (GDC) 和人类细胞图谱 (HCA) 我们的团队将利用这些经验和 为他们开发的软件，创建一个应用程序生态系统，满足他们的需求 AnVIL 并与其他 NIH 数据资源进行互操作，我们将通过以下目标来实现这一目标： ● 目标 1（软件工程）：利用现有软件功能创建用于存储、 在过去的五年里，我们的团队无限规模地共享和分析 AnVIL 数据集。 创建了一套模块化和开源软件功能，可以满足以下领域的关键需求 我们将利用这些现有的能力并将其扩展到新的方向。 解决与人类遗传学和功能基因组学相关的 AnVIL 特定科学目标。 ● 目标 2（数据工程）：整理数据和元数据资源，以便轻松使用它们 AnVIL 不仅是一套软件服务，而且还是一个巨大的存储库。 为了使该资源可供社区使用，它必须是基因型和表型信息。 我们将通过处理基因组数据集来实现这一目标。 使用一组一致的最佳实践管道，并将表型映射到通用数据模型。 ● 目标 3（运营）：为 AnVIL 社区建立并支持数据环境，以及 将其与其他 NIH 资源集成，作为 NIH 范围内的联合基因组数据共享的一部分。 Aim 1 的模块化组件是关键构建块，但仅靠它们还不足以满足 AnVIL 的需求；它们还必须作为服务建立并集成到一个连贯的实体中， 我们称之为“数据环境”。我们建议创建一个 AnVIL 数据环境，以实现 研究人员以安全、合规且简便的方式访问数据集。 这些努力的指导原则是，如果有一个方法，基因组科学的进步将会最快地发生。 为此，我们设计了由多个团体创建的多样性解决方案。 目标 1 的软件组件、管理目标 2 的数据集以及运营目标 3 的软件服务是 促进 AnVIL 周围的活动生态系统 我们的建议不仅侧重于创建和发展。 我们不仅自己运营软件服务，还建议整合第三方解决方案。 通过根据以下原则构建 AnVIL 数据环境来实现这一目标：(i) 模块化， (ii) 开放性，(iii) 社区参与，(iv) 标准化，以及 (v) 互操作性。