Börner Katy, Blood Philip D, Silverstein Jonathan C, Ruffalo Matthew, Satija Rahul, Teichmann Sarah A, Pryhuber Gloria, Misra Ravi S, Purkerson Jeffrey, Fan Jean, Hickey John W, Molla Gesmira, Xu Chuan, Zhang Yun, Weber Griffin, Jain Yashvardhan, Qaurooni Danial, Kong Yongxin, Bueckle Andreas, Herr Bruce W
Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA.
CIFAR MacMillan Multiscale Human program, CIFAR, Toronto, ON, Canada.
bioRxiv. 2024 Aug 14:2024.03.27.587041. doi: 10.1101/2024.03.27.587041.
The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.org) serves experimental datasets and supports data processing, search, filtering, and visualization. The Human Reference Atlas (HRA) Portal (https://humanatlas.io) provides open access to atlas data, code, procedures, and instructional materials. Experts from more than 20 consortia are collaborating to construct the HRA's Common Coordinate Framework (CCF), knowledge graphs, and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes, and biomarkers) and to use the HRA to understand changes that occur at each of these levels with aging, disease, and other perturbations. The 6th release of the HRA v2.0 covers 36 organs with 4,499 unique anatomical structures, 1,195 cell types, and 2,089 biomarkers (e.g., genes, proteins, lipids) linked to ontologies and 2D/3D reference objects. New experimental data can be mapped into the HRA using (1) three cell type annotation tools (e.g., Azimuth) or (2) validated antibody panels (OMAPs), or (3) by registering tissue data spatially. This paper describes the HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interface (APIs), flexible hybrid cloud infrastructure, and previews atlas usage applications.
人类生物分子图谱计划（HuBMAP）旨在构建一份健康成年人体的三维结构、细胞和分子参考图谱。HuBMAP数据门户（https://portal.hubmapconsortium.org）提供实验数据集，并支持数据处理、搜索、筛选和可视化。人类参考图谱（HRA）门户（https://humanatlas.io）提供对图谱数据、代码、程序和教学材料的开放访问。来自20多个联盟的专家正在合作构建HRA的通用坐标框架（CCF）、知识图谱以及描述人体多尺度结构（从器官和组织到细胞、基因和生物标志物）的工具，并利用HRA来了解随着衰老、疾病和其他扰动在这些层面上发生的变化。HRA v2.0的第6版涵盖36个器官，有4499个独特的解剖结构、1195种细胞类型以及2089种与本体和二维/三维参考对象相关联的生物标志物（如基因、蛋白质、脂质）。新的实验数据可以使用（1）三种细胞类型注释工具（如方位角工具）或（2）经过验证的抗体组（OMAPs），或（3）通过空间注册组织数据映射到HRA中。本文描述了HRA的用户案例、术语、数据格式、本体验证、统一分析工作流程、用户界面、教学材料、应用程序编程接口（API）、灵活的混合云基础设施，并预览了图谱使用应用程序。
