Data Exploration and Visualization Tools for HuBMAP and a Human Reference Atlas

HuBMAP 和人类参考图集的数据探索和可视化工具

• 批准号: 10886906
• 负责人: Nils Gehlenborg
• 金额: $ 175万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10886906
• 关键词: 3-Dimensional; Atlases; Biology; Cells; Communities; Data; Data Analyses; Genes; Human; Human BioMolecular Atlas Program; Human body; Maps; Medicine; Methods; Modernization; Pathway interactions; Phase; Production; Research; Tissues; Visual; Visualization; Visualization software; bioimaging; cellular imaging; data analysis pipeline; data exploration; data hub; data portal; data visualization; design; file format; genome browser; improved; public health relevance; tool; web-based tool

To enable the Human BioMolecular Atlas Program (HuBMAP) Consortium production phase, we will develop several new and improved spatial single cell and bioimaging data visualization features. These include Vitessce support for large volume 3D data combined with 2D maps, spatial queries in 2D maps via HuBMAP Data Portal UI and Vitessce, user workspaces with support for co-analysis of community and HuBMAP data, “datahubs” for external data that can be displayed in context of Human Reference Atlas and HuBMAP data, new file formats for 3D spatial data, deployment of generalized “cell x gene” matrix format across HuBMAP Data Portal, ability to store and share analyses of data conducted with analysis workspaces, integration of Vitessce with Common Coordinate Framework navigation tools, UI enhancements to scale to growing body of HuBMAP data (both in terms of volume and richness of the data and analysis results), seamless integration between evolving Human Reference Atlas UI and Data Portal UI. Furthermore, we will research solutions for (1) Seamless navigation through HuBMAP and integrated community data through visual interfaces that combine data portal UI, human reference atlas UI, and interactive visualization tools, e.g., Vitessce. (2) Extension of Vitessce to support interpretation of functional single-cell and tissue data through network and pathway visualizations that support 2D and 3D spatial information. (3) Rollout of “data hubs”, i.e., formats and annotation standards for spatial single-cell and tissue data that can be viewed in the context of the Human Reference Atlas (similar to “track hubs” for genome browsers). (4) UI-based analysis workspaces to assemble execution pipelines for data processing and visualization.

为了使人类生物分子图谱计划（HuBMAP）联盟的生产阶段，我们 我将开发几个新的和改进的空间单细胞和生物成像数据可视化 功能.其中包括Vitessce对大容量3D数据和2D数据的支持 地图，通过HuBMAP Data Portal UI和Vitessce在2D地图中进行空间查询，用户界面 支持社区和HuBMAP数据的共同分析，外部数据的“数据中心”， 可以在人类参考图谱和HuBMAP数据的上下文中显示， 3D空间数据，在HuBMAP数据中部署广义“细胞x基因”矩阵格式 门户网站，能够存储和共享通过分析工具进行的数据分析， Vitessce与通用坐标框架导航工具的集成、UI增强 扩展到不断增长的HuBMAP数据体（无论是在数据量和丰富性方面， 分析结果），不断发展的人类参考图谱UI和数据之间的无缝集成 门户用户界面。此外，我们还将研究解决方案（1）通过HuBMAP实现无缝导航 并通过可视化界面集成社区数据，该界面结合了联合收割机数据门户UI、人 参考图谱UI和交互式可视化工具，例如，Vitessce。(2)Vitessce的扩展 通过网络和通路支持功能性单细胞和组织数据的解释 支持2D和3D空间信息的可视化。(3)推出“数据中心”，格式 以及可以在上下文中查看的空间单细胞和组织数据的注释标准 人类参考图谱（类似于基因组浏览器的“跟踪中心”）。(4)基于ui 分析工具来组装用于数据处理和可视化的执行管道。