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; Ted Zhang; Zhou Yuan; Li Yao; Devin M. Wright; Seth Winfree; Christopher Werlein; Joel S. Welling; Clive H. Wasserfall; Xuefei ‘Julie’ Wang; Fusheng Wang; Ioannis S. Vlachos; Chad M. Vezina; David Van Valen; M. Todd Valerius; Jackie Uranic; Elizabeth L. Tsui; Jerin Easo Thomas; Tracey Theriault; Todd Theriault; Deanne M. Taylor; Purushothama Rao Tata; Ayako Suzuki; Christine Surrette; Joel C. Sunshine; Douglas W. Strand; Valentina Stanley; Jeffrey M. Spraggins; Michael Snyder; Dhruv Singhal; J. Alan Simmons; Kimberly Siletti; Kalyanam Shivkumar

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, Ted Zhang, Zhou YuanLi Yao, Devin M. Wright, Seth Winfree, Christopher Werlein, Joel S. Welling, Clive H. Wasserfall, Xuefei ‘Julie’ Wang, Fusheng Wang, Ioannis S. Vlachos, Chad M. Vezina, David Van Valen, M. Todd Valerius, Jackie Uranic, Elizabeth L. Tsui, Jerin Easo Thomas, Tracey Theriault, Todd Theriault, Deanne M. Taylor, Purushothama Rao Tata, Ayako Suzuki, Christine Surrette, Joel C. Sunshine, Douglas W. Strand, Valentina Stanley, Jeffrey M. Spraggins, Michael Snyder, Dhruv Singhal, J. Alan Simmons, Kimberly Siletti, Kalyanam Shivkumar,

^*Corresponding author for this work

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

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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., Zhang, T. (2025). Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nature Methods, 22(4), Article 171. https://doi.org/10.1038/s41592-024-02563-5

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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 = "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",

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

year = "2025",

month = apr,

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

language = "English",

volume = "22",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

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, Zhang, T, Yuan, Z, Yao, L, Wright, DM, Winfree, S, Werlein, C, Welling, JS, Wasserfall, CH, Wang, XJ, 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 2025, 'Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage', Nature Methods, vol. 22, no. 4, 171. 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 - 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

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.

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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

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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