National Institute of Diabetes and Digestive and Kidney Diseases ATLAS (D2K-ATLAS) Center as an accessible, comprehensive data portfolio for renal and genitourinary development and disease

国家糖尿病、消化和肾脏疾病研究所 ATLAS (D2K-ATLAS) 中心作为肾脏和泌尿生殖发育和疾病的可访问、全面的数据组合

• 批准号: 10708942
• 负责人: Sanjay Jain
• 金额: $ 162.05万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-25 至 2027-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10708942
• 关键词: Age; Anatomy; Atlases; Automation; Award; Big Data; Bioinformatics; Biological; Biological Markers; Biological Models; Biological Sciences; Biology; Cell Line; Cells; Characteristics; Collaborations; Communication; Communication Tools; Communities; Complex; Computer Analysis; Computer software; Computing Methodologies; Consensus; Data; Data Collection; Data Management Resources; Data Science; Data Set; Database Management Systems; Development; Digestive System Disorders; Discipline; Disease; Education; Educational workshop; FAIR principles; Female; Funding; Generations; Genitourinary system; Goals; Health; Histologic; Human; Human BioMolecular Atlas Program; Human Biology; Image; In Vitro; Information Dissemination; Kidney; Kidney Diseases; Knowledge; Learning; Link; Longevity; Lower urinary tract; Mission; Modernization; Molecular; Mus; National Institute of Diabetes and Digestive and Kidney Diseases; Ontology; Organ; Policies; Process; Public Health; Publications; Quality Control; Reference Standards; Reproducibility; Research; Research Personnel; Resolution; Scientist; Standardization; Testing; Three-Dimensional Image; Tissue Engineering; Training; United States National Institutes of Health; Vision; Visualization; Visualization software; Work; biological sex; body system; career; cell type; cloud based; comparative; complex data; computer studies; data access; data curation; data exploration; data integration; data modeling; data repository; data reuse; data structure; data submission; data visualization; diverse data; empowerment; experience; file format; flexibility; image visualization; improved; induced pluripotent stem cell; innovation; insight; male; multimodality; multiplexed imaging; ontology development; open source; operation; organ growth; outreach; programs; repository; sex; software development; tool; transcriptomics; usability; user-friendly; web app; web portal; web-based tool; website development

PROJECT SUMMARY Technical advancements have enabled the generation of large amounts of highly specialized and complex molecular data (e.g., single-cell transcriptomics and multiplex imaging) to study organ development, healthy and disease states, and differences between biological sexes at unprecedented scale and cellular resolution. This complexity introduces challenges in the organization and curation of these datasets and in applying computational methods. There is a need to provide accessible advanced analysis and visualization tools, and to utilize our domain knowledge to enable entry points for the research community to reuse data and ask new questions about human health and generate new hypotheses. Our overall objective is to create connections between molecular data of kidney and lower urinary tract present in GUDMAP, RBK, KPMP, HuBMAP (each consortium is represented on our team), so researchers with varying levels of experience can find relevant data, understand connections across model systems, and gain new insight by using provided analysis tools. Our vision is to establish the National Institute of Diabetes and Digestive and Kidney Diseases ATLAS (D2K-ATLAS) as a comprehensive data portfolio for renal and genitourinary development and disease. Curated data-driven reference data enables comparative analysis using advanced computational studies across various parameters, including sex, age, species, and healthy and disease settings. Providing analysis and visualization tools will aid knowledge transfer and broaden the usability of submitted data. Aim 1) Create a comprehensive, integrated, and F.A.I.R. cloud-based data management system integrating GUDMAP and RBK data, multi-species ontologies to facilitate cross-linkage of multi-study, multi-modality, and multi-consortia data, and web applications for data exploration and access. Aim 2) Implement web-based tools, data integration, human and mouse reference atlas, and data visualizations that enable researchers to interact with quality controlled, curated data for advanced analysis by developing processes, tools, and an access control policy for data collection, curation, publication, image annotation, quality control, analysis, and visualization. Aim 3) Administration, coordination, collaboration, dissemination, and outreach by our D2K-ATLAS Center, which will facilitate, communicate, and collaborate with the NIDDK, the GUDMAP/RBK Steering Committees and Consortium Management Boards, and investigators to achieve consortia goals, including education, outreach, and management of the Opportunity Pool awards. This effort will be significant because it provides curated reference datasets, establishes aligned data stewardship standards across the represented consortia and creates a consensus anatomical/cell type ontology linked to key biomarkers. Computational analysis is both an advancement and a barrier, requiring bioinformatics expertise. Our innovative proposal lowers these analysis barriers by providing layers of analysis and visualization tools for users of varied computational expertise and creates robust, data-driven reference standards for the research communities of mouse and human renal and genitourinary development and disease.

项目概要 技术进步使得产生大量高度专业化和复杂的 分子数据（例如单细胞转录组学和多重成像）来研究器官发育、健康和 疾病状态以及生物性别之间的差异以前所未有的规模和细胞分辨率。这 复杂性给这些数据集的组织和管理以及应用带来了挑战 计算方法。需要提供可访问的高级分析和可视化工具，并 利用我们的领域知识为研究社区提供重用数据和提出新问题的切入点 有关人类健康的问题并产生新的假设。我们的总体目标是建立联系 GUDMAP、RBK、KPMP、HuBMAP 中存在的肾脏和下尿路分子数据之间的关系（每个 我们的团队中有联盟代表），因此具有不同经验水平的研究人员可以找到相关数据， 了解模型系统之间的联系，并通过使用提供的分析工具获得新的见解。我们的愿景 旨在建立国家糖尿病、消化和肾脏疾病研究所 ATLAS (D2K-ATLAS) 作为 肾脏和泌尿生殖系统发育和疾病的综合数据组合。精心策划的数据驱动 参考数据可以使用各种参数的高级计算研究进行比较分析， 包括性别、年龄、物种以及健康和疾病环境。提供分析和可视化工具将有助于 知识转移并扩大所提交数据的可用性。目标 1) 创建一个综合性、综合性、 公平的。基于云的数据管理系统，集成GUDMAP和RBK数据，多物种本体 促进多研究、多模态、多联盟数据以及数据网络应用程序的交叉链接 探索和访问。目标 2) 实施基于网络的工具、数据集成、人类和小鼠参考图集， 和数据可视化，使研究人员能够与质量受控的、精心策划的数据进行交互，以实现高级 通过开发数据收集、管理、发布的流程、工具和访问控制策略来进行分析， 图像注释、质量控制、分析和可视化。目标 3) 管理、协调、协作、 我们的 D2K-ATLAS 中心将促进、沟通和合作 NIDDK、GUDMAP/RBK 指导委员会和联盟管理委员会以及调查人员 实现联盟目标，包括教育、推广和机会池奖项的管理。这 努力将是巨大的，因为它提供了精选的参考数据集，建立了一致的数据管理 代表联盟的标准，​​并创建与关键相关的共识解剖/细胞类型本体论 生物标志物。计算分析既是进步也是障碍，需要生物信息学专业知识。 我们的创新提案通过提供多层分析和可视化工具来降低这些分析障碍 用户拥有不同的计算专业知识，并为研究创建强大的、数据驱动的参考标准 小鼠和人类肾脏和泌尿生殖发育和疾病的群落。