HuBMAP Data Portal: A Resource for Multimodal Spatial and Single-Cell Data of Healthy Human Tissues

Area of Science:

• Human tissue atlasing
• Spatial and single-cell biology
• Bioinformatics and data science

Background:

• The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal is crucial for accessing multimodal human tissue data.
• Existing data repositories often lack comprehensive integration of spatial and single-cell information across multiple scales.
• Standardization and accessibility are key challenges in large-scale human tissue research.

Purpose of the Study:

• To describe the functionality, infrastructure, and design of the HuBMAP Data Portal.
• To highlight the portal's role in facilitating large-scale spatial single-cell research.
• To showcase the portal's capabilities for data search, discovery, visualization, and analysis.

Main Methods:

• Development of a comprehensive data repository for human tissue data.
• Implementation of infrastructure supporting data search, discovery, and visualization.
• Integration of uniform data processing pipelines and quality control measures.
• Provision of collaborative Workspaces with high-performance computing access.

Main Results:

• As of June 2026, the portal hosts 9,232 public datasets across 25 data types and 29 organ classes.
• The portal supports interactive visualizations (e.g., Vitessce) for non-spatial, 2D, and 3D spatial data.
• Uniform processing pipelines ensure data comparability across diverse samples and experiments.
• The portal facilitates metadata- and data-driven search for efficient data retrieval.

Conclusions:

• The HuBMAP Data Portal serves as a vital resource for the human spatial single-cell research community.
• Its integrated platform enhances data accessibility, comparability, and analytical capabilities.
• The portal supports collaborative research by providing access to high-performance computing and advanced visualization tools.