The evolution of the Human Reference Atlas continues. The release of the atlas’s fourth version – providing a more comprehensive, high-resolution, three-dimensional view of some of the 37 trillion cells in our human body -- offers the potential for medical advances in health, research and beyond.
The Luddy School of Informatics, Computing and Engineering’s Cyberinfrastructure for Network Science Center leads the HRA development and publication—in close collaboration with the HuBMAP HIVE and tissue experts around the globe.
“Atlas creation requires systematic collection of highest quality data, careful analysis and visualization of multi-scale datasets, and proactive engagement with diverse user communities interested in using the atlas to improve our understanding of the human body and human health,” said Katy Börner, Victor H. Yngve distinguished professor of engineering and information science, and CNS director.
The fourth version of the HRA, which provides an atlas of the human body down to the cellular level, has just been released with 13 updated anatomical structures, cell types, and biomarker tables (ASCT+B), two new 3D reference organs (left and right mammary glands), two updated 3D reference organs, 19 functional tissue units (FTUs) for nine organs and seven revised organ mapping antibody panels (OMAPs).
While the human genome is a one-dimensional structure and the DNA of any two people is 99 percent identical, the body is a three-dimensional structure that comes in many shapes and sizes. As a human ages, exercises, or gets sick, the number, type, size, and location of cells changes.
The HRA, along with its Common Coordinate Framework for a human body, aims to provide a unique address for each cell in the body. It’s similar to the latitude-longitude system used to navigate a world map. The HRA also provides standard terminologies and data structures for describing specimens, biological structures and spatial positions linked to existing ontologies.
The HRA -- https://humanatlas.io/release-notes/v1.3 -- now includes 57 three-dimensional reference organs with 1,588 anatomical structures. It lets users query and explore key anatomical structures, cell types and biomarkers down to the cellular level.
“The Human Reference Atlas will provide a comprehensive map of the human body,” said Bruce W. Herr II, senior software architect and project manager. “The current draft takes us from the outer body, progressing into organs, through to anatomical structures and functional tissue units, into the cell types that compose it all, and the biomarkers that help identify those cell types. The HRA is unique in tying all of these things together in a single, well-connected, open-source package.”
Every six months, a new version of the HRA data is released with the interfaces to visually explore the atlas, or access the data. The fifth release is set for June, 2023.
Learn more about the HRA
Learn about the data available in the HRA: https://humanatlas.io/overview-data
Learn how to explore the HRA: https://humanatlas.io/exploration-user-interface
Learn how to contribute data to the HRA: https://humanatlas.io/registration-user-interface
See HuBMAP’s Organ info pages for experimental data mapped to the Atlas: https://portal.hubmapconsortium.org/organ
Additional Reading
To learn more about the Human Reference Atlas (HRA) and the HRA, please read
- Snyder, Michael P., Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, and Zorina S. Galis. 2019. "The Human Body at Cellular Resolution: The NIH Human Biomolecular Atlas Program." Nature 574: 187-192. doi:10.1038/s41586-019-1629-x.
- Börner, Katy, Sarah A Teichmann, Ellen M Quardokus, James Gee, Kristen Browne, David Osumi-Sutherland, Bruce W Herr II, Andreas Bueckle, Hrishikesh Paul, Muzlifah A Haniffa, Laura Jardine, Amy Bernard, Song-Lin Ding, Jeremy A Miller, Shin Lin, Marc Halushka, Avinash Boppana, Teri A Longacre, John Hickey, Yiing Lin, M Todd Valerius, Yongqun He, Gloria Pryhuber, Xin Sun, Marda Jorgensen, Andrea J Radtke, Clive Wasserfall, Fiona Ginty, Jonhan Ho, Joel Sunshine, Rebecca T Beuschel, Maigan Brusko, Sujin Lee, Rajeev Malhotra, Sanjay Jain, and Griffin Weber. 2021. "Anatomical structures, cell types and biomarkers of the Human Reference Atlas." Nature Cell Biology 23: 1117-1128. doi: 10.1038/s41556-021-00788-6.
- Börner, Katy, Andreas Bueckle, Bruce W. Herr II, Leonard E. Cross, Ellen M. Quardokus, Elizabeth G. Record, Yingnan Ju, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Jeffrey M. Spraggins, and Griffin M. Weber. 2021. "Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas". bioRxiv doi: 10.1101/2021.12.30.474265. Accepted for Communications Biology.
- Börner, Katy, Ellen M. Quardokus, Bruce W. Herr II, Leonard E. Cross, Elizabeth G. Record, Yingnan Ju, Andreas D. Bueckle, James P. Sluka, Jonathan C. Silverstein, Kristen M. Browne, Sanjay Jain, Clive H. Wasserfall, Marda L. Jorgensen, Jeffrey M. Spraggins, Nathan H. Patterson, Mark A. Musen, and Griffin M. Weber. 2020. "Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies." arXiv:2007.14474v1.
Acknowledgments
The Human Reference Atlas (HRA) is under active development by the Indiana University Mapping Component as part of the HuBMAP HIVE and SenNet CODCC efforts with expert input by the HRA Editorial Board and in close collaboration with experts from more than 15 other consortia. Data was provided by the HIVE and TMC components of HuBMAP. Research has been funded by the NIH Common Fund through the Office of Strategic Coordination/Office of the NIH Director under HuBMAP Integration, Visualization, and Engagement (HIVE) component awards OT2OD033756 and OT2OD026671, by the Cellular Senescence Network (SenNet) Consortium through the Consortium Organization and Data Coordinating Center (CODCC) under award number U24CA268108, by the NIDDK Kidney Precision Medicine Project grant U2CDK114886, and the NIH National Institute of Allergy and Infectious Diseases (NIAID), Department of Health and Human Services under BCBB Support Services Contract HHSN316201300006W/HHSN27200002.