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
N1 - Publisher Copyright:
© The Author(s) 2025.
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 - https://www.scopus.com/pages/publications/105000833741
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 -