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

Morgan L. Turner,Thomas C. Smits,Tiffany S. Liaw,Brendan Honick,Bill Shirey,Lisa Choy,Nikolay Akhmetov,Sha An,David Betancur,Dominic Bordelon,Karl Burke,Ivan Cao-Berg,John Conroy,Christopher Csonka,P. Cuda,Sean Donahue,Stephen A. Fisher,Derek Furst,Edward Hanna,J. Hardi,Tabassum Kakar,Mark Keller,Xiang Li,Yan Ma,A. McWilliams,Austen Money,Richard S. Morgan,Eric Moerth,Juan Muerto,Mark A. Musen,Emily Nic,Martin J. O'Connor,Gesina Phillips,Alex Ropelewski,Ryan Sablosky,Sravani Saripalli,Max Sibilla,Derek Simmel,Alan Simmons,Xu Tang,Joel Welling,Zhou Yuan,Martin Hemberg,Matt Ruffalo,J. Silverstein,Philip D. Blood,Nils Gehlenborg Harvard Medical School,Boston,MA 02115,Pittsburgh Supercomputing Center,C. University,Pittsburgh,PA 15213,U. Pittsburgh,Pittsburgh PA 15260,Gene Lay Institute of immunology,Inflammation,Brigham,Women's Hospital,H. School,M. Hospital,U. Pennsylvania,Philadelphia,PA 19104,Stanford University,Stanford,CA 94305

Published 2025 in Unknown venue

ABSTRACT

The NIH Human BioMolecular Atlas Program (HuBMAP) Data Portal (https://portal.hubmapconsortium.org/) serves as a comprehensive repository for multi-modal spatial and single-cell data from healthy human tissues. This resource facilitates the NIH HuBMAP consortium's mission to create a widely accessible multi-scale spatial atlas of the healthy human body at single-cell resolution. As of October 2025, the portal hosts 5,032 datasets from 22 different data types spanning 27 organ classes across 310 donors. The portal's infrastructure and user interfaces enable efficient visualization and analysis directly in web browsers through integrated collaborative Jupyter workspaces and interactive Vitessce visualizations for over 1,500 non-spatial, 2D, and 3D spatial datasets. Uniform processing pipelines and rigorous quality control processes ensure comparability of results from different laboratories, organs, and donors for large-scale analyses, while externally processed, community-contributed datasets (EPICs) provide complementary perspectives. The portal interface supports both metadata- and data-driven search functionalities, bulk downloads, and integrated data collections, including supplementary data and visualizations for consortium publications.

PUBLICATION RECORD

  • Publication year

    2025

  • Venue

    Unknown venue

  • Publication date

    2025-11-07

  • Fields of study

    Biology, Medicine

  • Identifiers
    arXiv 2511.05708
  • External record

    Open on Semantic Scholar

  • Source metadata

    Semantic Scholar

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