Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage
Katy Börner, Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, Rahul Satija, Sarah A. Teichmann, Gloria Pryhuber, Ravi 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 J. Arends, Bruce J. Aronow, Rachel Bajema, Richard Baldock, Ross Barnowski, Daria Barwinska, Amy Bernard, David Betancur, Supriya Bidanta, Frida Björklund, Axel Bolin, Avinash Boppana, Luke Boulter, Kristen Browne, Maigan Brusko, Albert Burger, Martha Campbell‐Thompson, Ivan Cao-Berg, Anita R. Caron, Megan Carroll, Chrystal Chadwick, Hao Chen, Lu Chen, Bernard de Bono, Gail 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 Haniffa, Peter Hanna, Josef Hardi, Yongqun He, Brendan Honick, Derek Houghton, Maxim Itkin, Sanjay Jain, Laura Jardine, Z. Gordon Jiang, Yingnan Ju, Arivarasan Karunamurthy, Neil L. Kelleher, Timothy J. Kendall, Angela 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 Lundberg, Libby Maier, Rajeev Malhotra, Anna Martinez Casals, Anna Maria Masci, Clayton E. Mathews, Elizabeth McDonough, James Alastair McLaughlin, Rajasree Menon, Vilas Menon
Abstract
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.