Accès ouvert déclaré 2025 article

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

Katy Börner, Philip D. Blood, Jonathan C. Silverstein, Matthew Ruffalo, 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, 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, Jeremy A. Miller, Richard Morgan, Werner Müller, Robert F. Murphy, Mark A. Musen, Harikrishna Nakshatri, Martijn C. Nawijn, Elizabeth K. Neumann, Debra J. Nigra, Kathleen 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 J. 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 Singhal, M Snyder, Jeffrey M. Spraggins, Valentina Stanley, Douglas W. Strand, Joel Sunshine, Christine Surrette, Ayako Suzuki, Purushothama Rao Tata, Deanne Taylor, Todd N. Theriault, Tracey Theriault, Elizabeth Tsui, Jackie Uranic, M. Todd Valerius, David Van Valen, Chad M. Vezina, Ioannis S. Vlachos, Fusheng Wang, Xuefei Wang, Clive Wasserfall, Joel Welling, Christopher Werlein, Seth Winfree, Devin Wright, Yao Li, Yuan Zhou, Ted Zhang, Andreas Bueckle, Bruce W. Herr

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73Institutions déclarées

6Pays d’affiliation déclarés

Résumé fourni par la source

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.

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DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.

Titre Crossref: Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage
Date Crossref: 13/03/2025
Éditeur: Springer Science and Business Media LLC
Type: journal-article

Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude et ne compte pas comme une seconde source scientifique indépendante.

Institutions déclarées

Macmillan Cancer Support Indiana University Bloomington Pittsburgh Supercomputing Center Carnegie Mellon University University of Pittsburgh New York Genome Center Canadian Institute for Advanced Research Wellcome/MRC Cambridge Stem Cell Institute University of Cambridge University of Rochester Medicine Johns Hopkins University Duke University J. Craig Venter Institute Harvard University Weizmann Institute of Science Vanderbilt University Broad Institute University of Edinburgh Cincinnati Children's Hospital Medical Center California Institute of Technology Indiana University School of Medicine Indiana University – Purdue University Indianapolis The Kavli Foundation Stanford University National Institutes of Health National Institute of Allergy and Infectious Diseases University of Florida Heriot-Watt University European Bioinformatics Institute GE Global Research (United States)Stony Brook University University of Washington Allen Institute for Brain Science Allen Institute Richard L. Roudebush VA Medical Center Vanderbilt University Medical Center University of Pennsylvania University of Colorado Denver University of North Carolina at Chapel Hill Cleveland Clinic Wellcome Sanger Institute University of California, Los Angeles University of Michigan University of Pennsylvania Health System Washington University in St. Louis Newcastle University Beth Israel Deaconess Medical Center Northwestern University Lurie Children's Hospital University of California San Diego Lurie Children's Hospital Massachusetts General Hospital The University of Texas MD Anderson Cancer Center Columbia University Irving Medical Center Miltenyi Biotec (Germany)University Medical Center Groningen University of Groningen University of California, Davis Children's Hospital of Philadelphia Philadelphia University Columbia University VA Tennessee Valley Healthcare System Mass General Brigham UConn Health United States National Library of Medicine Buck Institute for Research on Aging Florida College University Medical Center Utrecht The University of Texas Southwestern Medical Center Johns Hopkins Medicine Brigham and Women's Hospital University of Wisconsin–Madison Medizinische Hochschule Hannover

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Sujets associés

Single-cell and spatial transcriptomicsCell Image Analysis TechniquesBioinformatics and Genomic Networks

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