Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage

作者：Katy Börner, Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, Rahul Satija, Sarah Amalia Teichmann, Gloria Pryhuber, Ravi S. Misra, Jeffrey M. Purkerson, Jean Fan, John W. Hickey, Gesmira Molla, Chuan Xu, Yun Zhang, Griffin M. Weber, Yashvardhan Jain, Danial Qaurooni, Yongxin Kong, HRA Team, Jakub Abramson, David M. Anderson, Kristin Ardlie, Mark Johan Arends, Bruce J. Aronow, Rachel Bajema, Richard Baldock, Ross Barnowski, Daria Barwinska, Amy Bernard, David Betancur, Supriya Bidanta, Frida Björklund, Axel Bolin, Avinash S. Boppana, Luke Boulter, Kristen Browne, Maigan A. Brusko, Albert Burger, Martha Campbell‐Thompson, Ivan Cao-Berg, Anita R. Caron, Megan Carroll, Chrystal M. Chadwick, Hao Chen, Lu Chen, Bernard de Bono, Gail H. Deutsch, Song‐Lin Ding, Sean P. Donahue, Tarek M. El‐Achkar, Adel Eskaros, Louis D. Falo, Melissa A. Farrow, Michael J. Ferkowicz, Stephen Fisher, James C. Gee, Ronald N. Germain, Michael Ginda, Fiona Ginty, Sarah A. Gitomer, Melanie B. Goldstone, Katherine S. Gustilo, James S. Hagood, Marc K. Halushka, Muzlifah A. Haniffa, Peter Hanna, Josef Hardi, Yongqun Oliver He, Brendan John Honick, Derek Houghton, Maxim G. Itkin, Sanjay R. Jain, Laura Jardine, Zhenghui Gordon Jiang, Yingnan Ju, Arivarasan D. Karunamurthy, Neil L. Kelleher, Timothy James Kendall, Angela R.S. Kruse, Monica M. Laronda, Louise C Laurent, Elisa Laurenti, Sujin Lee, Ed S. Lein, Chenran Li, Zhuoyan Li, Shin Lin, Yiing Lin, Scott A. Lindsay, Teri A. Longacre, Emma K. Lundberg, Libby Maier, Rajeev Kumar Malhotra, Anna Martinez Casals, Anna Maria Masci, Clayton E. Mathews, Elizabeth McDonough, James Alastair McLaughlin, Rajasree Menon, Vilas Menon, Jeremy A. Miller, Richard Morgan, Werner Müller, Robert F. Murphy, Mark A. Musen, Harikrishna Nakshatri, Martijn C. Nawijn, Elizabeth K. Neumann, Deb Nigra, Kathleen E. O’Neill, Mana M. Parast, U. M. Patel, Liming Pei, Hemali Phatnani, Gesina A. Phillips, Alison M. Pouch, Alvin C. Powers, Juan Puerto, Aleix Puig-Barbe, Ellen M. Quardokus, Andrea J. Radtke, Presha Rajbhandari, Elizabeth G. Record, Drucilla Jane Roberts, Alexander J. Ropelewski, David W. Rowe, Nancy Ruschman, Diane C. Saunders, Richard H. Scheuermann, Kevin L. Schey, Birgit Schilling, Heidi Schlehlein, Melissa Schwenk, Robin Scibek, Robert Seifert, Bill Shirey, Kalyanam Shivkumar, Kimberly Siletti, John K. Simmons, Dhruv K Singhal, Michael Snyder, Jeffrey M. Spraggins, Valentina Stanley, Douglas W. Strand, Joel C. Sunshine, Christine Surrette, Ayako Suzuki, Purushothama Rao Tata, Deanne M. Taylor, Todd N. Theriault, Tracey Theriault, Jerin Easo Thomas, Elizabeth L. Tsui, Jackie Uranic, M. Todd Valerius, David Van Valen, Chad M. Vezina, Ioannis S. Vlachos, Fusheng Wang, Xuefei Julie Wang, Clive Henry Wasserfall, Joel S. Welling, Christopher Werlein, Seth Winfree, Devin M. Wright, Yao Li, Yuan Zhou, Ted Zhang, Andreas Bueckle, Bruce W. Herr · 发表于：Nature Methods · 年份：2025 · DOI：10.1038/s41592-024-02563-5 · 被引用次数：42 · 研究领域：Single-cell and spatial transcriptomics、Cell Image Analysis Techniques、Bioinformatics and Genomic Networks

The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the multiscale structure of the human body (from organs and tissues down to cells, genes and biomarkers) and to use the HRA to characterize changes that occur with aging, disease and other perturbations. HRA v.2.0 covers 4,499 unique anatomical structures, 1,195 cell types and 2,089 biomarkers (such as genes, proteins and lipids) from 33 ASCT+B tables and 65 3D Reference Objects linked to ontologies. New experimental data can be mapped into the HRA using (1) cell type annotation tools (for example, Azimuth), (2) validated antibody panels or (3) by registering tissue data spatially. This paper describes HRA user stories, terminology, data formats, ontology validation, unified analysis workflows, user interfaces, instructional materials, application programming interfaces, flexible hybrid cloud infrastructure and previews atlas usage applications.