HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues

The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multimodal, multi-scale spatial and single-cell data from healthy human tissues. As of August 2026, the portal hosts 9,316 public datasets from 26 data types spanning 29 organ classes across 501 donors. Portal infrastructure and user interfaces support data search and discovery, visualization, and analysis directly in web browsers. These capabilities include metadata- and data-driven search, collaborative Workspaces with access to high-performance compute, and interactive Vitessce visualizations across non-spatial, 2D, and 3D spatial datasets. Data-type-specific uniform processing pipelines and rigorous quality control processes ensure comparability of results across laboratories, organs, and donors, while externally processed community-contributed datasets provide complementary perspectives. Here we describe portal functionality, infrastructure, and design, and highlight its role as a platform for large-scale spatial single-cell research across diverse data types, organs, and scales.

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Publication Details

Journal
Nature Communications
Published
2026-11-02
DOI
https://doi.org/10.1038/s41467-026-77835-z
Citations
4
Primary Topic
Single-cell and spatial transcriptomics
Type
article
Field-Weighted Citation Impact
6.87

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article

HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues

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4 citations
Nature Communications
Single-cell and spatial transcriptomics
6.87
article

HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues

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article en
4 citations

Abstract

The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multimodal, multi-scale spatial and single-cell data from healthy human tissues. As of August 2026, the portal hosts 9,316 public datasets from 26 data types spanning 29 organ classes across 501 donors. Portal infrastructure and user interfaces support data search and discovery, visualization, and analysis directly in web browsers. These capabilities include metadata- and data-driven search, collaborative Workspaces with access to high-performance compute, and interactive Vitessce visualizations across non-spatial, 2D, and 3D spatial datasets. Data-type-specific uniform processing pipelines and rigorous quality control processes ensure comparability of results across laboratories, organs, and donors, while externally processed community-contributed datasets provide complementary perspectives. Here we describe portal functionality, infrastructure, and design, and highlight its role as a platform for large-scale spatial single-cell research across diverse data types, organs, and scales.

Nature CommunicationsVol. 17(1)
Broad Institute (US), California Institute of Technology (US), Brigham and Women's Hospital (US), Beth Israel Deaconess Medical Center (US), Children's Hospital of Philadelphia (US), Harvard University (US), Pacific Northwest National Laboratory (US), University of Pittsburgh (US), Duke University (US), Vanderbilt University (US), University of Washington (US), Purdue University West Lafayette (US), University of Rochester Medical Center (US), University of Florida (US), Pittsburgh Supercomputing Center (US), University of California San Diego (US), University of Illinois Chicago (US), Massachusetts General Hospital (US), Indiana University Bloomington (US), National Institute of General Medical Sciences (US), University of Rochester (US), Indiana University (US), University at Buffalo, State University of New York (US), Carnegie Mellon University (US), University of Pennsylvania (US), The University of Texas at Austin (US), Leipzig University (DE), Stanford University (US)
National Institutes of Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Good health and well-being
Openalex Percentile: Top 4%
Single-cell and spatial transcriptomics
6.87
DOIOpen Access PDFOpenAlex
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