Human Reference Atlas

Overview

The Human Reference Atlas (HRA) is a comprehensive 3D spatial framework for mapping the healthy human body at single-cell resolution. Developed by the HuBMAP consortium and collaborators, the HRA provides standardized reference anatomical structures, cell type information, biomarkers, and spatial coordinates that enable integration and analysis of diverse biological data types.

Key Components

3D Reference Organs

• High-resolution 3D models of 11 organs
• Standardized anatomical structures and regions
• Common Coordinate Framework (CCF) for spatial registration

Cell Type Annotations

• Comprehensive cell type taxonomies
• Cell type biomarkers and signatures
• Linkages to molecular data

Biomarker Information

• Protein, gene, and lipid biomarkers
• Cell type-specific markers
• Spatial expression patterns

Data Model Features

• Common Coordinate Framework (CCF): 3D reference coordinate system for spatial data integration
• Anatomical Structures, Cell Types, and Biomarkers (ASCT+B): Structured tables linking anatomy, cell types, and biomarkers
• 3D Reference Object Library: Collection of validated 3D organ models
• Crosswalks: Mappings to standard ontologies (Uberon, CL, HGNC, etc.)

Scope and Coverage

• Organs: 11 major organs with 3D reference models
• Cell Types: Comprehensive coverage of human cell types
• Biomarkers: Thousands of molecular biomarkers
• Species: Human (Homo sapiens, NCBITaxon:9606)
• Resolution: Single-cell to organ level

Use Cases

• Spatially registering experimental datasets
• Cell type identification and validation
• Cross-dataset integration and comparison
• Atlas construction for healthy and diseased tissues
• Multi-omics data integration
• Precision medicine applications

Integration with HuBMAP

The HRA serves as the spatial reference framework for the Human BioMolecular Atlas Program (HuBMAP), enabling:

• Registration of tissue samples to standard anatomical locations
• Integration of multi-modal imaging and omics data
• Cross-consortium data sharing and comparison
• Reproducible analysis workflows

Information Resource ID

This resource has the Information Resource identifier: infores:hra

License and Reuse

HRA data and resources are released under CC BY 4.0 license, allowing free use with appropriate attribution.