Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2025 Mar 14

PMID 40082611

Authors

Katy Borner

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

Andreas Bueckle

Bruce W Herr 2nd

Affiliations

Soon will be listed here.

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.

Citing Articles

Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data.

Bueckle A, Herr 2nd B, Herr B, Hardi J, Quardokus E, Musen M bioRxiv. 2025; .

PMID: 39764040 PMC: 11703146. DOI: 10.1101/2024.12.22.630006.

A general strategy for generating expert-guided, simplified views of ontologies.

Caron A, Puig-Barbe A, Quardokus E, Balhoff J, Belfiore J, Chipampe N bioRxiv. 2025; .

PMID: 39763856 PMC: 11702530. DOI: 10.1101/2024.12.13.628309.

Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys.

Jain Y, Walsh C, Yagis E, Aslani S, Nandanwar S, Zhou Y bioRxiv. 2024; .

PMID: 39253466 PMC: 11383006. DOI: 10.1101/2024.08.25.609595.

Discovery of optimal cell type classification marker genes from single cell RNA sequencing data.

Liu A, Peng B, Pankajam A, Duong T, Pryhuber G, Scheuermann R bioRxiv. 2024; .

PMID: 38712147 PMC: 11071431. DOI: 10.1101/2024.04.22.590194.

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