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Lookup NU author(s): Dr Laura JardineORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© The Author(s) 2025. 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.
Author(s): Borner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber GJ, Misra RS, Purkerson JM, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber GM, Jain Y, Qaurooni D, Kong Y, Zhang T, Yuan Z, Yao L, Wright DM, Winfree S, Werlein C, Welling JS, Wasserfall CH, Wang X', Wang F, Vlachos IS, Vezina CM, Van Valen D, Valerius MT, Uranic J, Tsui EL, Thomas JE, Theriault T, Theriault T, Taylor DM, Tata PR, Suzuki A, Surrette C, Sunshine JC, Strand DW, Stanley V, Spraggins JM, Snyder M, Singhal D, Simmons JA, Siletti K, Shivkumar K, Shirey B, Seifert RP, Scibek R, Schwenk M, Schlehlein H, Schilling B, Schey KL, Scheuermann RH, Saunders DC, Ruschman NL, Rowe D, Ropelewski AJ, Roberts DJ, Record EG, Rajbhandari P, Radtke AJ, Quardokus EM, Puig-Barbe A, Puerto JF, Powers AC, Pouch AM, Phillips GA, Phatnani H, Pei L, Patel U, Parast MM, O'Neill K, Nigra DJ, Neumann EK, Nawijn MC, Nakshatri H, Musen MA, Murphy RF, Muller W, Morgan R, Miller JA, Menon V, Menon R, McLaughlin JA, McDonough E, Mathews CE, Masci AM, Martinez Casals A, Malhotra R, Maier L, Lundberg E, Longacre TA, Lindsay SA, Lin Y, Lin S, Li Z, Li C, Lein E, Lee S, Laurenti E, Laurent LC, Laronda MM, Kruse ARS, Kendall TJ, Kelleher NL, Karunamurthy A, Ju Y, Jiang ZG, Jardine L, Jain S, Itkin M, Houghton D, Honick BJ, He YO, Hardi J, Hanna P, Haniffa MA, Halushka MK, Hagood JS, Gustilo KS, Goldstone MB, Gitomer SA, Ginty F, Ginda M, Germain RN, Gee JC, Fisher SA, Ferkowicz MJ, Farrow M, Falo L, Eskaros A, El-Achkar TM, Donahue S, Ding S-L, Deutsch G, de Bono B, Chen L, Chen H, Chadwick C, Carroll M, Caron AR, Cao-Berg I, Campbell-Thompson M, Burger A, Brusko MA, Browne K, Boulter L, Boppana A, Bolin A, Bjorklund F, Bidanta S, Betancur D, Bernard A, Barwinska D, Barnowski R, Baldock RA, Bajema R, Aronow BJ, Arends MJ, Ardlie K, Anderson D, Abramson J, Bueckle A, Herr BW
Publication type: Article
Publication status: Published
Journal: Nature Methods
Year: 2025
Volume: 22
Pages: 845-860
Print publication date: 01/04/2025
Online publication date: 13/03/2025
Acceptance date: 11/11/2024
Date deposited: 10/04/2025
ISSN (print): 1548-7091
ISSN (electronic): 1548-7105
Publisher: Springer Nature
URL: https://doi.org/10.1038/s41592-024-02563-5
DOI: 10.1038/s41592-024-02563-5
Data Access Statement: All HuBMAP data are available via the HuBMAP Data Portal at https://portal.hubmapconsortium.org. Azimuth references can be accessed at https://azimuth.hubmapconsortium.org. HRA data and code are available at the HRA Portal (https://humanatlas.io). HuBMAP and HRA primary and secondary data repositories are listed in Supplementary Table 2 and HRA code repositories are in Supplementary Table 3. Code is available on three different GitHub organizations: (1) https://github.com/hubmapconsortium is the HuBMAP organization where HRA started; (2) https://github.com/cns-iu is the organization owned by the Cyberinfrastructure for Network Science Center at Indiana University and initial experimental HRA code starts here; and (3) https://github.com/x-atlas-consortia was created recently to host cross-consortia code, including hra-kg, hra-pop, hra-apps and hra-api. Supporting information is at https://cns-iu.github.io/hra-construction-usage-supporting-information.
PubMed id: 40082611
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