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; Albert Burger; Derek Houghton; 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
, Albert Burger

Derek Houghton, Andreas Bueckle, Bruce W. Herr

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

13 Citations (Scopus)

13 Downloads (Pure)

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
Pages (from-to)	845-860
Number of pages	16
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

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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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. 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 \{HRA Team\} and Albert Burger and Derek Houghton and Andreas Bueckle and Herr, \{Bruce W.\}",

year = "2025",

month = apr,

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

language = "English",

volume = "22",

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

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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 - Burger, Albert

AU - Houghton, Derek

AU - Bueckle, Andreas

AU - Herr, Bruce W.

PY - 2025/4

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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

SN - 1548-7091

VL - 22

SP - 845

EP - 860

JO - Nature Methods

JF - Nature Methods

IS - 4

ER -

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

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