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

HRA Team

doi:10.1038/s41592-024-02563-5

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

HRA Team

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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
Number of pages	16
Journal	Nature Methods
Volume	22
Issue number	4
DOIs	https://doi.org/10.1038/s41592-024-02563-5
State	Published - Apr 2025

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10.1038/s41592-024-02563-5

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@article{73eaf1b9545e42589da9f10a120cc99a,

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, 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 = "{HRA Team} and 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 Ted Zhang and Zhou Yuan and Li Yao and Wright, {Devin M.} and Seth Winfree and Christopher Werlein and Welling, {Joel S.} and Wasserfall, {Clive H.} and Wang, {Xuefei {\textquoteleft}Julie{\textquoteright}} and Fusheng Wang and Vlachos, {Ioannis S.} and Vezina, {Chad M.} and {Van Valen}, David and Valerius, {M. Todd} and Jackie Uranic and Tsui, {Elizabeth L.} and Thomas, {Jerin Easo} and Tracey Theriault and Todd Theriault and Taylor, {Deanne M.} and Tata, {Purushothama Rao} and Ayako Suzuki and Christine Surrette and Sunshine, {Joel C.} and Strand, {Douglas W.} and Valentina Stanley and Spraggins, {Jeffrey M.} and Michael Snyder and Dhruv Singhal and Simmons, {J. Alan} and Kimberly Siletti and Kalyanam Shivkumar and Bill Shirey and Seifert, {Robert P.} and Robin Scibek and Melissa Schwenk and Heidi Schlehlein and Birgit Schilling and Schey, {Kevin L.} and Scheuermann, {Richard H.} and Saunders, {Diane C.} and Ruschman, {Nancy L.} and David Rowe and Ropelewski, {Alexander J.} and Roberts, {Drucilla J.} and Record, {Elizabeth G.} and Presha Rajbhandari and Radtke, {Andrea J.} and Quardokus, {Ellen M.} and Aleix Puig-Barbe and Puerto, {Juan F.} and Powers, {Alvin C.} and Pouch, {Alison M.} and Phillips, {Gesina A.} and Hemali Phatnani and Liming Pei and Ushma Patel and Parast, {Mana M.} and Kathleen O{\textquoteright}Neill and Nigra, {Debra J.} and Neumann, {Elizabeth K.} and Nawijn, {Martijn C.} and Harikrishna Nakshatri and Musen, {Mark A.} and Murphy, {Robert F.} and Werner M{\"u}ller and Richard Morgan and Miller, {Jeremy A.} and Vilas Menon and Rajasree Menon and McLaughlin, {James A.} and Elizabeth McDonough and Mathews, {Clayton E.} and Masci, {Anna Maria} and {Martinez Casals}, Anna and Rajeev Malhotra and Libby Maier and Emma Lundberg and Longacre, {Teri A.} and Lindsay, {Scott A.} and Yiing Lin and Shin Lin and Zhuoyan Li and Chenran Li and Ed Lein and Sujin Lee and Elisa Laurenti and Laurent, {Louise C.} and Laronda, {Monica M.} and Kruse, {Angela R.S.} and Kendall, {Timothy J.} and Kelleher, {Neil L.} and Arivarasan Karunamurthy and Yingnan Ju and Jiang, {Z. Gordon} and Laura Jardine and Sanjay Jain and Maxim Itkin and Derek Houghton and Honick, {Brendan John} and He, {Yongqun Oliver} and Josef Hardi and Peter Hanna and Haniffa, {Muzlifah A.} and Halushka, {Marc K.} and Hagood, {James S.} and Gustilo, {Katherine S.} and Goldstone, {Melanie B.} and Gitomer, {Sarah A.} and Fiona Ginty and Michael Ginda and Germain, {Ronald N.} and Gee, {James C.} and Fisher, {Stephen A.} and Ferkowicz, {Michael J.} and Melissa Farrow and Louis Falo and Adel Eskaros and El-Achkar, {Tarek M.} and Sean Donahue and Ding, {Song Lin} and Gail Deutsch and {de Bono}, Bernard and Lu Chen and Haoran Chen and Chrystal Chadwick and Megan Carroll and Caron, {Anita R.} and Ivan Cao-Berg and Martha Campbell-Thompson and Albert Burger and Brusko, {Maigan A.} and Kristen Browne and Luke Boulter and Avinash Boppana and Axel Bolin and Frida Bj{\"o}rklund and Supriya Bidanta and David Betancur and Amy Bernard and Daria Barwinska and Ross Barnowski and Baldock, {Richard A.} and Rachel Bajema and Aronow, {Bruce J.} and Arends, {Mark J.} and Kristin Ardlie and David Anderson and Jakub Abramson and Andreas Bueckle and Herr, {Bruce W.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = apr,

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

language = "English",

volume = "22",

pages = "845--860",

journal = "Nature Methods",

issn = "1548-7091",

number = "4",

}

TY - JOUR

T1 - Human BioMolecular Atlas Program (HuBMAP)

T2 - 3D Human Reference Atlas construction and usage

AU - HRA Team

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 - Zhang, Ted

AU - Yuan, Zhou

AU - Yao, Li

AU - Wright, Devin M.

AU - Winfree, Seth

AU - Werlein, Christopher

AU - Welling, Joel S.

AU - Wasserfall, Clive H.

AU - Wang, Xuefei ‘Julie’

AU - Wang, Fusheng

AU - Vlachos, Ioannis S.

AU - Vezina, Chad M.

AU - Van Valen, David

AU - Valerius, M. Todd

AU - Uranic, Jackie

AU - Tsui, Elizabeth L.

AU - Thomas, Jerin Easo

AU - Theriault, Tracey

AU - Theriault, Todd

AU - Taylor, Deanne M.

AU - Tata, Purushothama Rao

AU - Suzuki, Ayako

AU - Surrette, Christine

AU - Sunshine, Joel C.

AU - Strand, Douglas W.

AU - Stanley, Valentina

AU - Spraggins, Jeffrey M.

AU - Snyder, Michael

AU - Singhal, Dhruv

AU - Simmons, J. Alan

AU - Siletti, Kimberly

AU - Shivkumar, Kalyanam

AU - Shirey, Bill

AU - Seifert, Robert P.

AU - Scibek, Robin

AU - Schwenk, Melissa

AU - Schlehlein, Heidi

AU - Schilling, Birgit

AU - Schey, Kevin L.

AU - Scheuermann, Richard H.

AU - Saunders, Diane C.

AU - Ruschman, Nancy L.

AU - Rowe, David

AU - Ropelewski, Alexander J.

AU - Roberts, Drucilla J.

AU - Record, Elizabeth G.

AU - Rajbhandari, Presha

AU - Radtke, Andrea J.

AU - Quardokus, Ellen M.

AU - Puig-Barbe, Aleix

AU - Puerto, Juan F.

AU - Powers, Alvin C.

AU - Pouch, Alison M.

AU - Phillips, Gesina A.

AU - Phatnani, Hemali

AU - Pei, Liming

AU - Patel, Ushma

AU - Parast, Mana M.

AU - O’Neill, Kathleen

AU - Nigra, Debra J.

AU - Neumann, Elizabeth K.

AU - Nawijn, Martijn C.

AU - Nakshatri, Harikrishna

AU - Musen, Mark A.

AU - Murphy, Robert F.

AU - Müller, Werner

AU - Morgan, Richard

AU - Miller, Jeremy A.

AU - Menon, Vilas

AU - Menon, Rajasree

AU - McLaughlin, James A.

AU - McDonough, Elizabeth

AU - Mathews, Clayton E.

AU - Masci, Anna Maria

AU - Martinez Casals, Anna

AU - Malhotra, Rajeev

AU - Maier, Libby

AU - Lundberg, Emma

AU - Longacre, Teri A.

AU - Lindsay, Scott A.

AU - Lin, Yiing

AU - Lin, Shin

AU - Li, Zhuoyan

AU - Li, Chenran

AU - Lein, Ed

AU - Lee, Sujin

AU - Laurenti, Elisa

AU - Laurent, Louise C.

AU - Laronda, Monica M.

AU - Kruse, Angela R.S.

AU - Kendall, Timothy J.

AU - Kelleher, Neil L.

AU - Karunamurthy, Arivarasan

AU - Ju, Yingnan

AU - Jiang, Z. Gordon

AU - Jardine, Laura

AU - Jain, Sanjay

AU - Itkin, Maxim

AU - Houghton, Derek

AU - Honick, Brendan John

AU - He, Yongqun Oliver

AU - Hardi, Josef

AU - Hanna, Peter

AU - Haniffa, Muzlifah A.

AU - Halushka, Marc K.

AU - Hagood, James S.

AU - Gustilo, Katherine S.

AU - Goldstone, Melanie B.

AU - Gitomer, Sarah A.

AU - Ginty, Fiona

AU - Ginda, Michael

AU - Germain, Ronald N.

AU - Gee, James C.

AU - Fisher, Stephen A.

AU - Ferkowicz, Michael J.

AU - Farrow, Melissa

AU - Falo, Louis

AU - Eskaros, Adel

AU - El-Achkar, Tarek M.

AU - Donahue, Sean

AU - Ding, Song Lin

AU - Deutsch, Gail

AU - de Bono, Bernard

AU - Chen, Lu

AU - Chen, Haoran

AU - Chadwick, Chrystal

AU - Carroll, Megan

AU - Caron, Anita R.

AU - Cao-Berg, Ivan

AU - Campbell-Thompson, Martha

AU - Burger, Albert

AU - Brusko, Maigan A.

AU - Browne, Kristen

AU - Boulter, Luke

AU - Boppana, Avinash

AU - Bolin, Axel

AU - Björklund, Frida

AU - Bidanta, Supriya

AU - Betancur, David

AU - Bernard, Amy

AU - Barwinska, Daria

AU - Barnowski, Ross

AU - Baldock, Richard A.

AU - Bajema, Rachel

AU - Aronow, Bruce J.

AU - Arends, Mark J.

AU - Ardlie, Kristin

AU - Anderson, David

AU - Abramson, Jakub

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, 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.

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, 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.

UR - http://www.scopus.com/inward/record.url?scp=105000833741&partnerID=8YFLogxK

U2 - 10.1038/s41592-024-02563-5

DO - 10.1038/s41592-024-02563-5

M3 - Article

C2 - 40082611

AN - SCOPUS:105000833741

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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