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 J. 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; Andreas Bueckle; Bruce W. Herr

doi:10.1038/s41592-024-02563-5

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 J. 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, Andreas Bueckle^*Bruce W. Herr^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	171
Pages (from-to)	845-860
Journal	Nature Methods
Volume	22
Issue number	4
Early online date	13 Mar 2025
DOIs	https://doi.org/10.1038/s41592-024-02563-5
Publication status	Published - Apr 2025

Keywords / Materials (for Non-textual outputs)

Atlases as Topic
Biomarkers
Humans
Imaging, Three-Dimensional/methods
Software
User-Computer Interface

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10.1038/s41592-024-02563-5Licence: CC BY

Human BioMolecular Atlas ProgramFinal published version, 4 MBLicence: Creative Commons: Attribution (CC-BY)

https://www.nature.com/articles/s41592-024-02563-5

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Börner, K., Blood, P. D., Silverstein, J. C., Ruffalo, M., Satija, R., Teichmann, S. A., Pryhuber, G. J., Misra, R. S., Purkerson, J. M., Fan, J., Hickey, J. W., Molla, G., Xu, C., Zhang, Y., Weber, G. M., Jain, Y., Qaurooni, D., Kong, Y., HRA Team, ... Herr, B. W. (2025). Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nature Methods, 22(4), 845-860. Article 171. https://doi.org/10.1038/s41592-024-02563-5

@article{801e90e05bf744bc8ac4f29279a25330,

title = "Human BioMolecular Atlas Program (HuBMAP):: 3D Human Reference Atlas construction and usage",

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, proteinsand 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 describesHRA 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.",

keywords = "Atlases as Topic, Biomarkers, Humans, Imaging, Three-Dimensional/methods, Software, User-Computer Interface",

author = "Katy B{\"o}rner and Blood, {Philip D.} and Silverstein, {Jonathan C.} and Matthew Ruffalo and Rahul Satija and Teichmann, {Sarah A.} and Pryhuber, {Gloria J.} and Misra, {Ravi S.} and Purkerson, {Jeffrey M.} and Jean Fan and Hickey, {John W.} and Gesmira Molla and Chuan Xu and Yun Zhang and Weber, {Griffin M.} and Yashvardhan Jain and Danial Qaurooni and Yongxin Kong and {HRA Team} and Jakub Abramson and David Anderson and Kristin Ardlie and Arends, {Mark J.} and Aronow, {Bruce J.} and Rachel Bajema and Baldock, {Richard a.} and Ross Barnowski and Daria Barwinska and Amy Bernard and David Betancur and Supriya Bidanta and Frida Bj{\"o}rklund and Axel Bolin and Avinash Boppana and Luke Boulter and Kristen Browne and Brusko, {Maigan a.} and Albert Burger and Martha Campbell-Thompson and Ivan Cao-Berg and Caron, {Anita r.} and Megan Carroll and Chrystal Chadwick and Haoran Chen and Lu Chen and {De bono}, Bernard and Gail Deutsch and Song-Lin Ding and Sean Donahue and El-Achkar, {Tarek m.} and Adel Eskaros and Louis Falo and Melissa Farrow and Ferkowicz, {Michael j.} and Fisher, {Stephen a.} and Gee, {James c.} and Germain, {Ronald n.} and Michael Ginda and Fiona Ginty and Gitomer, {Sarah a.} and Goldstone, {Melanie b.} and Gustilo, {Katherine s.} and Hagood, {James s.} and Halushka, {Marc k.} and Haniffa, {Muzlifah a.} and Peter Hanna and Josef Hardi and He, {Yongqun oliver} and Honick, {Brendan john} and Derek Houghton and Maxim Itkin and Sanjay Jain and Laura Jardine and Jiang, {Z. gordon} and Yingnan Ju and Arivarasan Karunamurthy and Kelleher, {Neil l.} and Kendall, {Timothy j.} and Kruse, {Angela r. s.} and Laronda, {Monica m.} and Laurent, {Louise c.} and Elisa Laurenti and Sujin Lee and Ed Lein and Chenran Li and Zhuoyan Li and Shin Lin and Yiing Lin and Lindsay, {Scott a.} and Longacre, {Teri a.} and Emma Lundberg and Libby Maier and Rajeev Malhotra and {Martinez casals}, Anna and Masci, {Anna maria} and Mathews, {Clayton e.} and Elizabeth Mcdonough and Mclaughlin, {James a.} and Rajasree Menon and Vilas Menon and Miller, {Jeremy a.} and Richard Morgan and Werner M{\"u}ller and Murphy, {Robert f.} and Musen, {Mark a.} and Harikrishna Nakshatri and Nawijn, {Martijn c.} and Neumann, {Elizabeth k.} and Nigra, {Debra j.} and Kathleen O{\textquoteright}neill and Parast, {Mana m.} and Ushma Patel and Liming Pei and Hemali Phatnani and Phillips, {Gesina a.} and Pouch, {Alison m.} and Powers, {Alvin c.} and Puerto, {Juan f.} and Aleix Puig-Barbe and Quardokus, {Ellen m.} and Radtke, {Andrea j.} and Presha Rajbhandari and Record, {Elizabeth g.} and Roberts, {Drucilla j.} and Ropelewski, {Alexander j.} and David Rowe and Ruschman, {Nancy l.} and Saunders, {Diane c.} and Scheuermann, {Richard h.} and Schey, {Kevin l.} and Birgit Schilling and Heidi Schlehlein and Melissa Schwenk and Robin Scibek and Seifert, {Robert p.} and Bill Shirey and Kalyanam Shivkumar and Kimberly Siletti and Simmons, {J. alan} and Dhruv Singhal and Michael Snyder and Spraggins, {Jeffrey m.} and Valentina Stanley and Strand, {Douglas w.} and Sunshine, {Joel c.} and Christine Surrette and Ayako Suzuki and Tata, {Purushothama rao} and Taylor, {Deanne m.} and Todd Theriault and Tracey Theriault and Thomas, {Jerin easo} and Tsui, {Elizabeth l.} and Jackie Uranic and Valerius, {M. todd} and {Van valen}, David and Vezina, {Chad m.} and Vlachos, {Ioannis s.} and Fusheng Wang and Wang, {Xuefei {\textquoteleft}julie{\textquoteright}} and Wasserfall, {Clive h.} and Welling, {Joel s.} and Christopher Werlein and Seth Winfree and Wright, {Devin m.} and Li Yao and Zhou Yuan and Ted Zhang and Andreas Bueckle and Herr, {Bruce W.}",

year = "2025",

month = apr,

doi = "10.1038/s41592-024-02563-5",

language = "English",

volume = "22",

pages = "845--860",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "4",

}

Börner, 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, HRA Team, Bueckle, A & Herr, BW 2025, 'Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage', Nature Methods, vol. 22, no. 4, 171, pp. 845-860. https://doi.org/10.1038/s41592-024-02563-5

TY - JOUR

T1 - Human BioMolecular Atlas Program (HuBMAP):

T2 - 3D Human Reference Atlas construction and usage

AU - Börner, Katy

AU - Blood, Philip D.

AU - Silverstein, Jonathan C.

AU - Ruffalo, Matthew

AU - Satija, Rahul

AU - Teichmann, Sarah A.

AU - Pryhuber, Gloria J.

AU - Misra, Ravi S.

AU - Purkerson, Jeffrey M.

AU - Fan, Jean

AU - Hickey, John W.

AU - Molla, Gesmira

AU - Xu, Chuan

AU - Zhang, Yun

AU - Weber, Griffin M.

AU - Jain, Yashvardhan

AU - Qaurooni, Danial

AU - Kong, Yongxin

AU - HRA Team

AU - Abramson, Jakub

AU - Anderson, David

AU - Ardlie, Kristin

AU - Arends, Mark J.

AU - Aronow, Bruce J.

AU - Bajema, Rachel

AU - Baldock, Richard a.

AU - Barnowski, Ross

AU - Barwinska, Daria

AU - Bernard, Amy

AU - Betancur, David

AU - Bidanta, Supriya

AU - Björklund, Frida

AU - Bolin, Axel

AU - Boppana, Avinash

AU - Boulter, Luke

AU - Browne, Kristen

AU - Brusko, Maigan a.

AU - Burger, Albert

AU - Campbell-Thompson, Martha

AU - Cao-Berg, Ivan

AU - Caron, Anita r.

AU - Carroll, Megan

AU - Chadwick, Chrystal

AU - Chen, Haoran

AU - Chen, Lu

AU - De bono, Bernard

AU - Deutsch, Gail

AU - Ding, Song-Lin

AU - Donahue, Sean

AU - El-Achkar, Tarek m.

AU - Eskaros, Adel

AU - Falo, Louis

AU - Farrow, Melissa

AU - Ferkowicz, Michael j.

AU - Fisher, Stephen a.

AU - Gee, James c.

AU - Germain, Ronald n.

AU - Ginda, Michael

AU - Ginty, Fiona

AU - Gitomer, Sarah a.

AU - Goldstone, Melanie b.

AU - Gustilo, Katherine s.

AU - Hagood, James s.

AU - Halushka, Marc k.

AU - Haniffa, Muzlifah a.

AU - Hanna, Peter

AU - Hardi, Josef

AU - He, Yongqun oliver

AU - Honick, Brendan john

AU - Houghton, Derek

AU - Itkin, Maxim

AU - Jain, Sanjay

AU - Jardine, Laura

AU - Jiang, Z. gordon

AU - Ju, Yingnan

AU - Karunamurthy, Arivarasan

AU - Kelleher, Neil l.

AU - Kendall, Timothy j.

AU - Kruse, Angela r. s.

AU - Laronda, Monica m.

AU - Laurent, Louise c.

AU - Laurenti, Elisa

AU - Lee, Sujin

AU - Lein, Ed

AU - Li, Chenran

AU - Li, Zhuoyan

AU - Lin, Shin

AU - Lin, Yiing

AU - Lindsay, Scott a.

AU - Longacre, Teri a.

AU - Lundberg, Emma

AU - Maier, Libby

AU - Malhotra, Rajeev

AU - Martinez casals, Anna

AU - Masci, Anna maria

AU - Mathews, Clayton e.

AU - Mcdonough, Elizabeth

AU - Mclaughlin, James a.

AU - Menon, Rajasree

AU - Menon, Vilas

AU - Miller, Jeremy a.

AU - Morgan, Richard

AU - Müller, Werner

AU - Murphy, Robert f.

AU - Musen, Mark a.

AU - Nakshatri, Harikrishna

AU - Nawijn, Martijn c.

AU - Neumann, Elizabeth k.

AU - Nigra, Debra j.

AU - O’neill, Kathleen

AU - Parast, Mana m.

AU - Patel, Ushma

AU - Pei, Liming

AU - Phatnani, Hemali

AU - Phillips, Gesina a.

AU - Pouch, Alison m.

AU - Powers, Alvin c.

AU - Puerto, Juan f.

AU - Puig-Barbe, Aleix

AU - Quardokus, Ellen m.

AU - Radtke, Andrea j.

AU - Rajbhandari, Presha

AU - Record, Elizabeth g.

AU - Roberts, Drucilla j.

AU - Ropelewski, Alexander j.

AU - Rowe, David

AU - Ruschman, Nancy l.

AU - Saunders, Diane c.

AU - Scheuermann, Richard h.

AU - Schey, Kevin l.

AU - Schilling, Birgit

AU - Schlehlein, Heidi

AU - Schwenk, Melissa

AU - Scibek, Robin

AU - Seifert, Robert p.

AU - Shirey, Bill

AU - Shivkumar, Kalyanam

AU - Siletti, Kimberly

AU - Simmons, J. alan

AU - Singhal, Dhruv

AU - Snyder, Michael

AU - Spraggins, Jeffrey m.

AU - Stanley, Valentina

AU - Strand, Douglas w.

AU - Sunshine, Joel c.

AU - Surrette, Christine

AU - Suzuki, Ayako

AU - Tata, Purushothama rao

AU - Taylor, Deanne m.

AU - Theriault, Todd

AU - Theriault, Tracey

AU - Thomas, Jerin easo

AU - Tsui, Elizabeth l.

AU - Uranic, Jackie

AU - Valerius, M. todd

AU - Van valen, David

AU - Vezina, Chad m.

AU - Vlachos, Ioannis s.

AU - Wang, Fusheng

AU - Wang, Xuefei ‘julie’

AU - Wasserfall, Clive h.

AU - Welling, Joel s.

AU - Werlein, Christopher

AU - Winfree, Seth

AU - Wright, Devin m.

AU - Yao, Li

AU - Yuan, Zhou

AU - Zhang, Ted

AU - Bueckle, Andreas

AU - Herr, Bruce W.

PY - 2025/4

Y1 - 2025/4

N2 - 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, proteinsand 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 describesHRA 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.

AB - 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, proteinsand 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 describesHRA 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.

KW - Atlases as Topic

KW - Biomarkers

KW - Humans

KW - Imaging, Three-Dimensional/methods

KW - Software

KW - User-Computer Interface

U2 - 10.1038/s41592-024-02563-5

DO - 10.1038/s41592-024-02563-5

M3 - Article

C2 - 40082611

SN - 1548-7091

VL - 22

SP - 845

EP - 860

JO - Nature Methods

JF - Nature Methods

IS - 4

M1 - 171

ER -

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

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Keywords / Materials (for Non-textual outputs)

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