Alliance Central: A platform for sustainable development of next generation genome knowledgebases

Alliance Central：下一代基因组知识库可持续发展的平台

• 批准号: 10020426
• 负责人: CAROL J BULT
• 金额: $ 500万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-18 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10020426
• 关键词: Adopted; Adoption; Animal Model; Basic Science; Biological; Biological Models; Biology; Biomedical Research; Caenorhabditis elegans; Communication; Communities; Computer software; Data; Data Commons; Data Reporting; Data Science; Databases; Development; Disease; Drosophila genus; Ecosystem; Educational workshop; FAIR principles; Feedback; Fostering; Generations; Genes; Genetic; Genome; Genomics; Goals; Health; Hour; Human; Human Biology; Human Genome; Human Resources; Individual; Infrastructure; Ingestion; Internet; Knowledge; Laboratory mice; Leadership; Literature; Maintenance; Methods; Mission; Modeling; Modernization; Ontology; Organism; Orthologous Gene; Pattern; Practice Management; Process; Proteins; Rattus; Readability; Research Personnel; Resource Development; Resource Informatics; Resources; Saccharomycetales; Software Tools; Source; Standardization; Structure; Students; Sustainable Development; Testing; Training; Training Programs; Translational Research; United States National Institutes of Health; Variant; XenBase; Zebrafish; application programming interface; base; comparative genomics; data analysis pipeline; data archive; data format; data harmonization; data management; data mining; data resource; data sharing; data standards; data submission; gene function; genome browser; genome resource; genomic data; human disease; improved; innovation; knowledge base; member; model organisms databases; next generation; operation; outreach; response; sharing platform; software development; structured data; tool; tool development; usability; web app; web site; working group

Project Summary The Alliance of Genome Resources (the Alliance) is a “knowledge commons” for expertly curated genomic data and annotations provided by model organism databases (MODs) and the Gene Ontology Consortium (GOC). Our mission is to facilitate the use of model organisms to understand human biology and disease. The Alliance is organized as two interconnected functional units: Alliance Central and Alliance Knowledge Centers. Alliance Central is responsible for development and maintenance of the software platform and shared modular infrastructure and for the coordination of data harmonization activities across the Knowledge Centers. Alliance Knowledge Centers such as the MODs and the GOC are responsible for expert curation and for submission of data to Alliance Central using common data formats. Knowledge Centers also are responsible for organism- specific user support activities, resources, and user access to data not yet supported by Alliance Central. This U24 application seeks support for the activities of Alliance Central. The proposal reflects a new and transformational approach to modernizing the MOD/GOC ecosystem, increasing the impact and utility of essential community genome resources, and optimizing operational efficiencies for knowledgebases. The aims build on the significant accomplishments we achieved as a consortium since we launched the Alliance in 2016, including: a common management and governance structure, Working Groups, multiple channels for communications among consortium members, infrastructure for coordinated software development and version control, data sharing with the NIH Data Commons Pilot initiative, the development of a common set of orthologs, the release of the Alliance web site and APIs, and successful development of software components that have been adopted by both Alliance members and external resources. Our focus for Specific Aim 1 will be on implementing a shared platform for ingesting, storing, and harmonizing data for MODs. We will continue our long-standing commitment to data management practices that align with FAIR principles. In Specific Aim 2 we describe our plans to implement common methods, including well-documented APIs, for access to model organism data and annotations. The deliverables for this aim will foster widespread adoption and use of Alliance data and resources for the development of new applications for biological discovery and translational research. In Specific Aim 3 we describe our plans to implement a framework to support the development and deployment of software applications, workflows, and analysis tools that use model organism data and annotations. The enhanced functionality for comparative genomics fostered by these innovations will empower the biomedical research community to leverage knowledge across multiple organisms for hypothesis generation and pattern discovery. Finally, in Specific Aim 4 we describe the management and organization of the Alliance as well as the planned activities of our centralized user support helpdesk.

项目摘要 基因组资源联盟（Alliance of Genome Resources）是一个专家管理的基因组数据的“知识共享区 以及模式生物数据库（MOD）和基因本体论联盟（GOC）提供的注释。 我们的使命是促进利用模式生物来了解人类生物学和疾病。联盟 联盟由两个相互关联的功能单元组成：联盟中心和联盟知识中心。联盟 中心负责开发和维护软件平台和共享模块 基础设施和协调知识中心的数据统一活动。联盟 知识中心，如国防部和GOC负责专家策展和提交 使用通用数据格式将数据传输到Alliance Central。知识中心也负责有机体- Alliance Central尚未支持的特定用户支持活动、资源和用户对数据的访问。这 U24申请寻求对联盟中心活动的支持。该提案反映了一个新的和 现代化MOD/GOC生态系统的转型方法，增加 重要的社区基因组资源，并优化知识库的运营效率。目标 在我们自2016年启动联盟以来作为一个联盟所取得的重大成就的基础上， 包括：共同的管理和治理结构、工作组、 联合体成员之间的通信，协调软件开发的基础设施和版本 控制，与NIH数据共享试点计划共享数据，开发一套共同的直系同源物， 联盟网站和API的发布，以及软件组件的成功开发， 已被联盟成员和外部资源采用。我们的具体目标1的重点将是 实施共享平台，用于为MOD输入、存储和协调数据。我们将继续 长期致力于符合FAIR原则的数据管理实践。具体目标2 描述了我们实现通用方法的计划，包括有良好文档记录的API，用于访问模型 生物体数据和注释。这一目标的交付成果将促进Alliance的广泛采用和使用 数据和资源，用于开发生物发现和转化研究的新应用。 在具体目标3中，我们描述了我们实施框架以支持开发和部署的计划 使用模式生物数据和注释的软件应用程序、工作流程和分析工具。的 这些创新所促进的比较基因组学功能的增强将使生物医学 研究界利用跨多个生物体的知识进行假设生成和模式 的发现最后，在具体目标4中，我们描述了联盟的管理和组织，以及 我们的集中用户支持帮助台的计划活动。