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（联盟）是专业策划基因组数据的“知识共享” 以及模型生物数据库（MOD）和基因本体论联盟（GOC）提供的注释。 我们的任务是促进使用模型生物来了解人类生物学和疾病。联盟 被组织为两个相互联系的功能单元：联盟中央和联盟知识中心。联盟 中央负责软件平台的开发和维护并共享模块化 基础架构以及整个知识中心的数据协调活动的协调。联盟 知识中心（例如mod和GOC）负责实验策划和提交 使用通用数据格式向联盟中心的数据数据。知识中心也负责生物 - 特定的用户支持活动，资源和用户访问Alliance Central尚未支持的数据。这 U24申请寻求支持联盟中央活动的支持。该提案反映了一个新的和 变革型方法来现代化mod/goc生态系统，增加 基本的社区基因组资源，并优化知识库的运营效率。目的 自从我们在2016年启动联盟以来，我们作为一个财团取得的重大成就的基础 包括：共同管理和治理结构，工作组，多个渠道 财团成员之间的通信，用于协调软件开发和版本的基础架构 控制，使用NIH数据共享的数据共享飞行员倡议，开发一组直系同源物， 联盟网站和API的发布，以及成功开发具有的软件组件 联盟成员和外部资源都采用了我们。我们对特定目标1的重点将是 实施共享平台，以摄入，存储和协调mod的数据。我们将继续我们的 长期以来对与公平原则保持一致的数据管理实践的承诺。在特定目标2中我们 描述我们实施通用方法（包括有据可查的API）的计划，以访问模型 生物数据和注释。此目标的可交付成果将促进采用和使用联盟 用于开发新应用的数据和资源，用于生物发现和翻译研究。 在特定目标3中，我们描述了我们实施支持开发和部署的框架的计划 使用模型有机体数据和注释的软件应用程序，工作流和分析工具。这 这些创新促进的比较基因组学的功能增强将增强生物医学的能力 研究社区利用多种生物体的知识进行假设的产生和模式 发现。最后，在特定目标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服务台的计划活动。