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

项目摘要 基因组资源联盟(The Alliance of Genome Resources，简称联盟)是一个专门管理基因组数据的“知识共享空间” 以及由模型生物数据库(MODS)和基因本体论联盟(GOC)提供的注释。 我们的使命是促进使用模型生物来了解人类生物学和疾病。《联盟》 由两个相互关联的职能单位组成：联盟中心和联盟知识中心。联盟 中央负责软件平台和共享模块的开发和维护 这些资源将用于基础设施建设和协调各知识中心的数据统一活动。联盟 知识中心，如国防部和GOC，负责专家管理和提交 使用通用数据格式将数据发送到联盟中心。知识中心还负责有机体- 特定的用户支持活动、资源和对Alliance Central尚不支持的数据的用户访问。这 U24申请寻求对联盟中心活动的支持。该提案反映了一种新的和 实现MOD/GOC生态系统现代化的转型方法，提高 基本的社区基因组资源，并优化知识库的运行效率。目标 在我们作为一个联盟自2016年启动联盟以来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、多渠道 联盟成员之间的沟通、协调软件开发和版本的基础设施 控制，与NIH数据共享试点计划共享数据，开发一套通用的同源基因， 发布联盟网站和应用程序界面，并成功开发具有 已被联盟成员和外部资源采纳。我们针对特定目标1的重点将放在 实施用于接收、存储和协调MODS数据的共享平台。我们将继续我们的 长期致力于符合公平原则的数据管理做法。在具体目标2中，我们 描述我们为访问模型而实施通用方法的计划，包括文档齐全的API 生物体数据和注释。实现这一目标的成果将促进联盟的广泛采用和使用 用于开发生物发现和转化研究新应用的数据和资源。 在具体目标3中，我们描述了实施框架以支持开发和部署的计划 使用模型有机体数据和注释的软件应用程序、工作流程和分析工具。这个 由这些创新促进的比较基因组学的增强功能将使生物医学 研究社区利用跨多个有机体的知识来生成假设和模式 发现号。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服务台计划的活动。

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.