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Prof. Dr. Katy Börner Connects Anatomy and Disease with the Multiscale Human Reference Atlas
The Berlin Institute of Health at Charité (BIH) is pleased to welcome Prof. Dr. Katy Börner as a new Visiting Fellow. The internationally renowned scientist has been working at the BIH since June 2025 for a period of three years as part of the “Visiting Fellow” program funded by the Charité Foundation. Her project, “Multiscale Human Reference Atlas – An Ontological Bridge Between Anatomy and Disease,” aims to interlink the detailed anatomical mapping of the Human Reference Atlas (HRA) with the Human Phenotype Ontology (HPO), which describes disease phenotypes and is led by BIH Professor Peter Robinson. By establishing a systematic, multiscale digital map of the human body, Börner’s work seeks to deepen the understanding of the relationship between healthy anatomical structures and pathological changes, thereby advancing research, diagnosis, and the development of personalized therapies.
Why did you choose the Berlin Institute of Health at Charité (BIH), and what does your project involve?
The Human Reference Atlas (HRA) is a multiscale, multimodal, three-dimensional atlas of the anatomical structures and cells in the healthy human body [1, 2]. The HRA provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies. The associated Common Coordinate Framework (CCF)—akin to the latitude-longitude system of Earth—supports data aggregation across scales and demographics. More than 25 consortia from around the globe are contributing to the HRA.
The Stiftung Charité funding will make it possible to interconnect the HRA and HPO knowledge graphs in support of novel expanded functionality for both efforts.
The joint project will build a bridge between detailed anatomical reference data and phenotypic information in diseases. It creates new opportunities for researching the causes of illnesses, improving diagnostic methods, and developing personalized therapies. The linkage makes it possible to combine spatially precise anatomical data with standardized disease characteristics, thereby enabling a better understanding of complex biological relationships.
The Berlin Institute of Health at Charité (BIH) is particularly well suited for this endeavor because it operates at the interface of biomedical basic research, clinical application, and digital innovation.
What are the challenges of building interdisciplinary bridges between computer science, medicine, and biology?
Different disciplines use different terminology, have different cultures and value systems. In the Intelligent Systems Engineering Department at Indiana University, we embrace renaissance engineering—a close integration of art, science, and engineering—inspired by Leonardo da Vinci and others who applied an interdisciplinary approach to solve problems. For the Human Reference Atlas, we organize monthly working group meetings to bring different experts together (e.g., surgeons, pathologists, anatomists, single cell researchers, ontology experts, computer scientists, engineers), to discuss user needs, technological advances, novel methods, data, and tools; and to collectively agree on the best process to construct and use the evolving HRA. The atlas is intended for researchers, educators, students, medical professionals, and decision-makers who want to understand, compare, and apply biomedical data in research, clinical practice, or education. On November 5, 2025, we will have the 68th open meeting. All experts are welcome to attend; please register here to receive an invitation with more information.
Why is visualizing complex biomedical data important for research, clinical practice, and the public?
Human physiology unfolds across spatial and temporal scales in three dimensions. The below figure illustrates the multiscale, 3D nature of the HRA—from whole body (macro) to functional tissue units (renal corpuscle in kidney, meso) to proteins and genes (micro).
To map and model this multiscale complexity in support of precision medicine and precision health, it is important to use highest quality data and code, plus the expertise of the global research community to arrive at a human reference atlas that properly represents human diversity and is maximally useful for biomedical research and clinical practice. Data visualizations make it possible to explore data across scales, to communicate insights across disciplinary boundaries, and to share scientific advances with general audiences.
How does dialogue with clinics, public institutions, and the population take shape within your project?
Clinicians, pathologists, surgeons, and other clinical experts are making major contributions to the construction and usage of human atlases. Public events such as in-person presentations in libraries or science museums or virtual presentations in online events such as the 24 hour long the “Human Reference Atlas Event” in 2022 or the “Multiscale Human Event” in 2024 introduce the HRA effort via engaging talks, behind-the-scenes videos, and interactive tool demonstration. They aim to share the pleasures of scientific discovery, to create excitement for the power and value of science, and to inspire others to join and/or support the HRA effort.
How do patients benefit from your research?
HRA can be used to study how cell type populations (i.e., the number and types of cells) change in different tissues as we age or when disease strikes. Diseases frequently change local cell neighborhoods, e.g., what cells are close to which other cell types. An example for lung was published in a recent Nature Methods paper [2] and is reproduced here.
It compares the distribution of parenchymal cells (including endothelial, epithelial, and muscle) that compose the blood vessels, airways, and gas exchanging functional lung structures and resident immune cells including macrophages, to local vasculature (called VCCF Vis) using the Cell Distance Explorer tool. Healthy tissue data is shown on top and diseased on bottom. The multiplexed immunofluorescence microscopy images show bronchiole (br) and an accompanying the small pulmonary artery (pa). Scale bars are rendered in white indicating 5 mm; red 200 µm; and yellow 100 µm. Cell distance distribution graphs on the right present healthy lung (top) and diseased BPD lung (bottom). The violin plot (middle) compares distance distributions for cell types common in both datasets. The Cell Distance Explorer is freely available and has been used to systematically quantify and visualize distances between different cell types. This makes it possible to analyze changes in cell neighborhoods and tissue organization, for example, caused by aging or diseases, in detail.
Talking Biography
On October 16, Prof. Börner will be leading a networking event on career planning, reconciliation of work and family life, but also moments of success and challenges of the career path, for female, trans*, inter* and non-binary scientists who are in the early or intermediate stages of their career. Find out how to sign up here.
Publications
- Börner, Katy, Sarah A. Teichmann, Ellen M. Quardokus, et al. 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, Philip Blood, Jonathan C. Silverstein, et al. 2025. "Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage". Nature Methods 22: 845–860. doi: 10.1038/s41592-024-02563-5.