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Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage
Katy Börner1,2, Philip D Blood3, Jonathan C Silverstein4
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA. katy@iu.edu.
Nature Methods
|March 14, 2025
Summary
The Human BioMolecular Atlas Program created a 3D Human Reference Atlas (HRA) detailing human anatomy, cell types, and biomarkers. This comprehensive atlas aids in understanding healthy and perturbed biological states.
Area of Science:
- Biomedical Informatics
- Human Anatomy
- Molecular Biology
Background:
- The Human BioMolecular Atlas Program (HuBMAP) initiative aims to create a comprehensive 3D Human Reference Atlas (HRA).
- This atlas serves as a foundational resource for understanding human biology at multiple scales.
Purpose of the Study:
- To describe the architecture and components of the HRA v.2.0.
- To outline methods for integrating new experimental data into the HRA.
- To detail the infrastructure and applications supporting HRA utilization.
Main Methods:
- Development of a Common Coordinate Framework (CCF) and knowledge graphs.
- Integration of 33 ASCT+B tables and 65 3D Reference Objects linked to ontologies.
- Utilization of cell type annotation tools, antibody panels, and spatial registration for data mapping.
Main Results:
- HRA v.2.0 encompasses 4,499 anatomical structures, 1,195 cell types, and 2,089 biomarkers.
- Established standardized terminology, data formats, and ontology validation processes.
- Developed user interfaces, APIs, and cloud infrastructure for atlas access and analysis.
Conclusions:
- The HRA provides a scalable, multiscale framework for human biology research.
- It facilitates the characterization of biological changes in aging and disease.
- The described infrastructure supports diverse applications and data integration for the HuBMAP project.
