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Related Experiment Video

Updated: Jun 24, 2025

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands

Reconstruction of 3-Dimensional Histology Volume and its Application to Study Mouse Mammary Glands

Published on: July 26, 2014

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

Katy Börner^1,2, Philip D Blood³, Jonathan C Silverstein⁴

¹Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA.

Biorxiv : the Preprint Server for Biology

|June 3, 2024

Summary

The Human Reference Atlas (HRA) provides a comprehensive 3D map of the human body, integrating molecular and cellular data. This resource aids in understanding human biology and disease across multiple scales.

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Area of Science:

Biomedical informatics
Human anatomy
Molecular biology

Background:

The Human BioMolecular Atlas Program (HuBMAP) initiative aims to create a detailed reference atlas of the healthy adult human body.
Existing data and tools for human atlasing are fragmented, necessitating a unified framework.

Purpose of the Study:

To describe the Human Reference Atlas (HRA) v2.0, its components, and integration strategies.
To outline the infrastructure and methodologies supporting the HRA's development and accessibility.
To detail user-centric features and applications of the HRA for biological research.

Main Methods:

Development of a Common Coordinate Framework (CCF) and knowledge graphs for multiscale human body structure.
Integration of experimental datasets via cell type annotation tools, antibody panels, and spatial registration.
Establishment of standardized ontologies, data formats, and unified analysis workflows.

Main Results:

The HRA v2.0 release encompasses 36 organs, 4,499 anatomical structures, 1,195 cell types, and 2,089 biomarkers.
The HRA Portal offers open access to atlas data, code, and instructional materials.
Multiple methods are available for mapping new experimental data into the HRA framework.

Conclusions:

The HRA provides a foundational resource for understanding human biology and disease.
Standardized data integration and accessibility are key to advancing human atlasing efforts.
The HRA infrastructure supports diverse applications in biomedical research and discovery.