HuBMAP Data Portal: a resource for multimodal 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; Shaokun An; David Betancur; Dominic Bordelon; Karl Burke; Ivan Cao-Berg; John Conroy; Chris Csonka; Penny Cuda; Sean Donahue; Stephen Fisher; Derek Furst; Ed Hanna; Josef Hardi; Tabassum Kakar; Mark S. Keller; Devin Lange; Xiang Li; Yan Ma; Alison McWilliams; Austen Money; Richard Morgan; Eric Moerth; Juan Muerto; Mark A. Musen; Emily Nic; Martin J. O'Connor; Gesina Phillips; Alexander J. Ropelewski; Ryan Sablosky; Sravani Saripalli; Max Sibilla; Derek Simmel; Alan Simmons; Xu Tang; Joel Welling; Zhou Yuan; Martin Hemberg; HuBMAP Consortium; Matthew Ruffalo; Jonathan Silverstein; Philip Blood; Nils Gehlenborg

arXiv · 2511.05708

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

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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.

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Morgan L. Turner, Thomas C. Smits, Tiffany S. Liaw, Brendan Honick, Bill Shirey, Lisa Choy, Nikolay Akhmetov, Shaokun An, David Betancur, Dominic Bordelon, Karl Burke, Ivan Cao-Berg, John Conroy, Chris Csonka, Penny Cuda, Sean Donahue, Stephen Fisher, Derek Furst, Ed Hanna, Josef Hardi, Tabassum Kakar, Mark S. Keller, Devin Lange, Xiang Li, Yan Ma, Alison McWilliams, Austen Money, Richard Morgan, Eric Moerth, Juan Muerto, Mark A. Musen, Emily Nic, Martin J. O'Connor, Gesina Phillips, Alexander J. Ropelewski, Ryan Sablosky, Sravani Saripalli, Max Sibilla, Derek Simmel, Alan Simmons, Xu Tang, Joel Welling, Zhou Yuan, Martin Hemberg, HuBMAP Consortium, Matthew Ruffalo, Jonathan Silverstein, Philip Blood, Nils Gehlenborg. 2025-11-07. HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues. https://arxiv.org/abs/2511.05708

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