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

被引：2

作者：

Borner, Katy ^{[1
,2
]}

Blood, Philip D. ^{[3
]}

Silverstein, Jonathan C. ^{[4
]}

Ruffalo, Matthew ^{[5
]}

Satija, Rahul ^{[6
]}

Teichmann, Sarah A. ^{[2
,7
,8
]}

Pryhuber, Gloria J. ^{[9
]}

Misra, Ravi S. ^{[9
]}

Purkerson, Jeffrey M. ^{[9
]}

Fan, Jean ^{[10
]}

Hickey, John W. ^{[11
]}

Molla, Gesmira ^{[6
]}

Xu, Chuan ^{[7
]}

Zhang, Yun ^{[12
]}

Weber, Griffin M. ^{[13
]}

Jain, Yashvardhan ^{[1
]}

Qaurooni, Danial ^{[1
]}

Kong, Yongxin ^{[1
]}

Bueckle, Andreas ^{[1
]}

Herr, Bruce W., II ^{[1
]}

Abramson, Jakub ^{[14
]}

Anderson, David ^{[15
]}

Ardlie, Kristin ^{[16
]}

Arends, Mark J. ^{[17
]}

Aronow, Bruce J. ^{[18
]}

Bajema, Rachel ^{[19
]}

Baldock, Richard A. ^{[17
]}

Barnowski, Ross ^{[20
]}

Barwinska, Daria ^{[21
]}

Bernard, Amy ^{[22
]}

Betancur, David ^{[3
]}

Bidanta, Supriya ^{[19
]}

Bjorklund, Frida ^{[23
]}

Bolin, Axel ^{[19
]}

Boppana, Avinash ^{[19
]}

Boulter, Luke ^{[17
]}

Browne, Kristen ^{[24
]}

Brusko, Maigan A. ^{[25
]}

Burger, Albert ^{[26
]}

Campbell-Thompson, Martha ^{[25
]}

Cao-Berg, Ivan ^{[3
]}

Caron, Anita R. ^{[27
]}

Carroll, Megan ^{[3
]}

Chadwick, Chrystal ^{[28
]}

Chen, Haoran ^{[29
]}

Chen, Lu ^{[30
]}

de Bono, Bernard ^{[21
]}

Deutsch, Gail ^{[31
]}

Ding, Song-Lin ^{[32
]}

Donahue, Sean ^{[29
]}

机构：

[1] Indiana Univ, Dept Intelligent Syst Engn, Luddy Sch Informat Comp & Engn, Bloomington, IN 47405 USA

[2] CIFAR, MacMillan Multiscale Human Program, Toronto, ON, Canada

[3] Carnegie Mellon Univ, Pittsburgh Supercomp Ctr, Pittsburgh, PA USA

[4] Univ Pittsburgh, Dept Biomed Informat, Sch Med, Pittsburgh, PA USA

[5] Carnegie Mellon Univ, Ray & Stephanie Lane Computat Biol Dept, Pittsburgh, PA USA

[6] New York Genome Ctr, New York, NY USA

[7] Univ Cambridge, Jeffrey Cheah Biomed Ctr, Cambridge Stem Cell Inst, Cambridge Biomed Campus, Cambridge, England

[8] Univ Cambridge, Dept Med, Cambridge, England

[9] Univ Rochester, Med Ctr, Rochester, NY USA

[10] Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD USA

[11] Duke Univ, Dept Biomed Engn, Durham, NC USA

[12] J Craig Venter Inst, La Jolla, CA USA

[13] Harvard Med Sch, Dept Biomed Informat, Boston, MA USA

[14] Weizmann Inst Sci, Rehovot, Israel

[15] Vanderbilt Univ, Nashville, TN USA

[16] Broad Inst, Cambridge, MA USA

[17] Univ Edinburgh, Edinburgh, Midlothian, Scotland

[18] Cincinnati Childrens Hosp Med Ctr, Cincinnati, OH USA

[19] Indiana Univ, Bloomington, IN USA

[20] CALTECH, Pasadena, CA USA

[21] Indiana Univ Sch Med, Indianapolis, IN USA

[22] Kavli Fdn, Los Angeles, CA USA

[23] Stanford Univ, Stanford, CA USA

[24] NIAID, NIH, Buffalo, NY USA

[25] Univ Florida, Gainesville, FL USA

[26] Heriot Watt Univ, Edinburgh, Midlothian, Scotland

[27] EMBL EBI, Hinxton, Cambs, England

[28] GE HealthCare Technol & Innovat Ctr, Niskayuna, NY USA

[29] Carnegie Mellon Univ, Pittsburgh, PA USA

[30] SUNY Stony Brook, Stony Brook, NY USA

[31] Univ Washington, Seattle, WA USA

[32] Allen Inst Brain Sci, Seattle, WA USA

[33] Indianapolis VA Med Ctr, Indianapolis, IN USA

[34] Vanderbilt Univ, Med Ctr, Nashville, TN USA

[35] Univ Pittsburgh, Pittsburgh, PA USA

[36] Vanderbilt Univ, Sch Med, Nashville, TN USA

[37] Univ Penn, Philadelphia, PA USA

[38] NIAID, NIH, Bethesda, MD USA

[39] Univ Colorado, Sch Med, Aurora, CO USA

[40] Univ North Carolina Chapel Hill, Chapel Hill, NC USA

[41] Cleveland Clin Fdn, Cleveland, OH USA

[42] Wellcome Sanger Inst, Cambridge, England

[43] Univ Calif Los Angeles, Los Angeles, CA USA

[44] Univ Michigan, Ann Arbor, MI USA

[45] Pittsburgh Supercomp Ctr, Pittsburgh, PA USA

[46] Univ Penn, Penn Med, Philadelphia, PA USA

[47] Washington Univ St Louis, St Louis, MO USA

[48] Newcastle Univ, Newcastle Upon Tyne, Tyne & Wear, England

[49] Beth Israel Deaconess Med Ctr, Boston, MA USA

[50] Harvard Med Sch, Boston, MA USA

来源：

NATURE METHODS | 2025年

关键词：

FUNCTIONAL TISSUE UNITS; FOUNDATIONAL MODEL; ANATOMY;

D O I：

10.1038/s41592-024-02563-5

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：845 / 860

页数：22

共 127 条

[21]

Bueckle A., 2022, Using a millitome, DOI [10.5281/zenodo.7382703, DOI 10.5281/ZENODO.7382703]

[22]

Bueckle A., 2023, Front. Bioinform., V3, DOI [10.1101/2023.02.13.528002, DOI 10.1101/2023.02.13.528002]

[23]

Bueckle A., 2022, Zenodo, DOI [10.5281/zenodo.5942601, DOI 10.5281/ZENODO.14346542]

[24]

Bueckle A., 2024, HRA Organ Gallery in VR

[25]

Caron A. R., 2024, PREPRINT, DOI DOI 10.1101/2024.12.13.628309

[26]

Chan Zuckerberg Initiative, 2022, Chan Zuckerberg CELLxGENE Discover

[27]

Chen HR, 2024, bioRxiv, DOI [10.1101/2024.03.08.584082, 10.1101/2024.03.08.584082, DOI 10.1101/2024.03.08.584082]

[28] Evaluation of cell segmentation methods without reference segmentations [J].

Chen, Haoran ;

Murphy, Robert F. .

MOLECULAR BIOLOGY OF THE CELL, 2023, 34 (06)

[29] Real-Time Spatial Registration for 3D Human Atlas [J].

Chen, Lu ;

Teng, Dejun ;

Zhu, Tian ;

Kong, Jun ;

Herr, Bruce W., II ;

Bueckle, Andreas ;

Boerner, Katy ;

Wang, Fusheng .

PROCEEDINGS OF THE 10TH ACM SIGSPATIAL INTERNATIONAL WORKSHOP ON ANALYTICS FOR BIG GEOSPATIAL DATA, BIGSPATIAL 2022, 2022, :27-35

[30] STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping [J].

Clifton, Kalen ;

Anant, Manjari ;

Aihara, Gohta ;

Atta, Lyla ;

Aimiuwu, Osagie K. ;

Kebschull, Justus M. ;

Miller, Michael I. ;

Tward, Daniel ;

Fan, Jean .

NATURE COMMUNICATIONS, 2023, 14 (01)

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