Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

IF 32.1 1区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Nature Methods Pub Date : 2025-03-13 DOI:10.1038/s41592-024-02563-5

Katy Börner, Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, Rahul Satija, Sarah A. Teichmann, Gloria J. Pryhuber, Ravi S. Misra, Jeffrey M. Purkerson, Jean Fan, John W. Hickey, Gesmira Molla, Chuan Xu, Yun Zhang, Griffin M. Weber, Yashvardhan Jain, Danial Qaurooni, Yongxin Kong, HRA Team, Andreas Bueckle, Bruce W. Herr II

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Abstract

The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a 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 characterize changes that occur with aging, disease and other perturbations. HRA v.2.0 covers 4,499 unique anatomical structures, 1,195 cell types and 2,089 biomarkers (such as genes, proteins and lipids) from 33 ASCT+B tables and 65 3D Reference Objects linked to ontologies. New experimental data can be mapped into the HRA using (1) cell type annotation tools (for example, Azimuth), (2) validated antibody panels or (3) by registering tissue data spatially. This paper describes HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interfaces, flexible hybrid cloud infrastructure and previews atlas usage applications. This Resource describes data, code and tools developed for the Human Reference Atlas and the Human BioMolecular Atlas Program for building and navigating a multiscale human atlas.

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人类生物分子图谱程序（HuBMAP）：三维人类参考图谱的构建和使用。

人类生物分子图谱计划（HuBMAP）旨在构建健康成人身体的三维人类参考图谱（HRA）。来自20多个联盟的专家合作开发了一个通用坐标框架（CCF）、知识图谱和工具，用于描述人体的多尺度结构（从器官和组织到细胞、基因和生物标志物），并使用HRA来表征衰老、疾病和其他扰动所发生的变化。HRA v.2.0涵盖了来自33个ASCT+B表和65个与本体相关的3D参考对象的4,499个独特解剖结构，1,195个细胞类型和2,089个生物标志物（如基因，蛋白质和脂质）。新的实验数据可以使用(1)细胞类型注释工具（例如Azimuth），(2)经过验证的抗体面板或(3)通过空间注册组织数据映射到HRA中。本文描述了HRA用户故事、术语、数据格式、本体验证、统一分析工作流、用户界面、教学材料、应用程序编程接口、灵活的混合云基础设施，并预览了地图集使用应用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nature Methods 生物-生化研究方法

CiteScore

58.70

自引率

1.70%

发文量

326

审稿时长

1 months

期刊介绍： Nature Methods is a monthly journal that focuses on publishing innovative methods and substantial enhancements to fundamental life sciences research techniques. Geared towards a diverse, interdisciplinary readership of researchers in academia and industry engaged in laboratory work, the journal offers new tools for research and emphasizes the immediate practical significance of the featured work. It publishes primary research papers and reviews recent technical and methodological advancements, with a particular interest in primary methods papers relevant to the biological and biomedical sciences. This includes methods rooted in chemistry with practical applications for studying biological problems.