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

基本信息

批准号：
10683183
负责人：
CAROL J BULT
金额：
$ 499.5万
依托单位：
CALIFORNIA INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
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/10683183
关键词：
Adopted Adoption Basic Science Biological Biological Models Biology Biomedical Research Caenorhabditis elegans Collaborations Communication Communities Computer software Data Data Commons Data Reporting Data Science Databases Dedications 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 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 community engagement comparative genomics data analysis pipeline data archive data format data harmonization data management data mining data sharing data standards data submission empowerment gene function genome browser genome resource genomic data human disease improved innovation knowledge commons knowledgebase member model organism model organisms databases next generation operation outreach response sharing platform software development structured data tool tool development usability web app web site working group

项目摘要

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.

项目概要基因组资源联盟（联盟）是专业策划的基因组数据的“知识共享区” 以及由模式生物数据库 (MOD) 和基因本体联盟 (GOC) 提供的注释。我们的使命是促进利用模型生物来了解人类生物学和疾病。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。 Central负责软件平台和共享模块的开发和维护基础设施以及协调整个知识中心联盟的数据协调活动。 MOD 和 GOC 等知识中心负责专家策划和提交使用通用数据格式将数据传输至联盟中心知识中心还负责有机体。 Alliance Central 尚不支持特定的用户支持活动、资源和用户对数据的访问。 U24申请寻求对Alliance Central活动的支持，该提案体现了一种新的方式。 MOD/GOC 生态系统现代化的变革方法，提高影响力和效用重要的社区基因组资源，并优化知识库的运营效率。自 2016 年成立联盟以来，我们作为一个联盟取得了重大成就，包括：共同的管理和治理结构、工作组、多种渠道联盟成员之间的通信、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、开发一组通用的直向同源物、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纳，我们的具体目标 1 的重点将是：实施一个用于摄取、存储和协调 MOD 数据的共享平台。在具体目标 2 中，我们长期致力于符合公平原则的数据管理实践。描述我们实施通用方法的计划，包括详细记录的 API，以访问模型该目标的可交付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生物数据和注释的软件应用程序、工作流程和分析工具。这些创新促进的比较基因组学的增强将增强生物医学的能力研究界利用跨多种生物体的知识来生成假设和模式最后，在具体目标 4 中，我们描述了联盟的管理和组织以及我们集中用户支持服务台的计划活动。