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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.

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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.

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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 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.