HuBMAP Human Reference Atlas Workshop

Summary

The Human Reference Atlas (HRA) is a multiscale, multimodal, three-dimensional atlas of the anatomical structures and cells in the healthy human body. The HRA provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies. This workshop brought together experts from the Kidney Precision Medicine Project (KPMP), the Human Phenotype Ontology (HPO), and HuBMAP to share and integrate human atlas data and code across efforts.

Location

Intelligent Systems Engineering Department

Luddy School of Informatics, Computing, and Engineering

700 N. Woodlawn Ave, Bloomington, IN 47408, USA

https://cns.iu.edu/visitor_info.html

Date

August 25-26, 2025

References

Gargano MA et al (2024) The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2024 PMID: 37953324; https://pubmed.ncbi.nlm.nih.gov/37953324
Börner, Katy, Philip Blood, Jonathan C. Silverstein, et al. 2025. "Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage". Nature Methods. doi: 10.1038/s41592-024-02563-5. https://www.nature.com/articles/s41597-025-05183-6

Goals

Share HRA data across atlas efforts.
Use HRA lightweight components and other HRA code in other portals.
Expand utility of existing HRA Jupyter notebooks.
Explore connecting the HRA with disease via HPO and KPMP.
Continue the development of the KPMP-HuBMAP integration work started at a previous hackathon.
Identify synergies across human atlas efforts.

Participants

KPMP Team

Yongqun Oliver He, Prof, University of Michigan
Jie Zheng, Staff, University of Michigan
Ruopeng Wu, Student, University of Michigan
Yichao Chen, Student, University of Michigan

HPO Team

Aybuge Altay, Postdoc, Berlin Institute of Health at Charité (BIH) Center of Health Data Sciences

Indiana University Team

Katy Börner, CNS and HRA lead
Bruce W. Herr II, System Architect
Andreas Bueckle, Research Lead and HRApop Lead
Michael Ginda, NLP & HRAlit Expert

Results

Over the two days, many discussions and significant development took place. Key results include:

We identified six data sources that will be interlinked: HRA ASCT+B relationships, HRApop experimental data, HRAlit publications data, DISCO+KPMP+HuBMAP experimental data, HPO, and KTAO.
Five key concepts will be used to interconnect the data: Anatomical Structures, Cell Types, Biomarkers, Phenotypes, and Diseases.
Work was started to generate node and edge files from these sources to be used as input in creating a knowledge graph to answer biological questions about kidney diseases and disease biomarkers.
The DISCO Kidney Atlas and the KPMP-HuBMAP project will be interlinked for data validation or full integration.
Initial groundwork has been laid out to determine the overlap between genes reported by the Ontology of Genes and Genomes (OGG), HRApop, and HPO.
New publication opportunities were identified to capture the output and insights from the Hackathon.

Acknowledgements

We thank Peter Robinson and Wiebke Hartung at Berlin Institute of Health at Charité and Meryl S. Jacob, Elizabeth Record, and Jill L. Clancy at Indiana University.

Prior CCF/HRA Workshops