Human reference atlas improves cell type annotations across organs and tools
Compiling, Validating, and Using Human Reference Atlas Cell Type Annotation Crosswalks
Human-Computer Interaction
Summary
Different tools label the types of cells in human organs, but their names often don’t match up, making it hard to compare results. The authors created a set of maps, called crosswalks, connecting cell type names from 10 different tools to a common set based on a cell ontology. They combined these maps into one ‘Supertree’ that helps researchers compare data from many organs and technologies. This work makes it easier to build and use detailed human cell atlases by standardizing how cell types are named and connected.
What this means in practice
- •For bioinformatics teams: Integrate cell type annotations from multiple tools into a unified framework for consistent analysis across organs and technologies.
- •For clinical data analysts: Compare cell type data from various spatial and molecular profiling methods for better interpretation of tissue samples.
Authors
Nicole Vasilevsky, Aleix Puig-Barbe, Andreas Bueckle, Ellen M. Quardokus, Yongxin Kong, Divya Prasanth Paraman, Jie Zheng, Yongqun He, Yashvardhan Jain, Bruce W. Herr, Katy Börner
Abstract
The Human Reference Atlas (HRA) v2.5 includes 4,807 anatomical structures, 1,347 cell types, and 2,215 biomarkers (genes, proteins, lipids); 81 organs with 1,392 anatomical structures modeled in three dimensions (3D). Mapping new data into the HRA requires 3D spatial registration and/or cell type annotation (CTann). Many CTann tools exist but few use cell type names linked to Cell Ontology (CL), making comparisons across tools, tissues, and organs difficult. The HRA supports five transcriptomics CTann tools (Azimuth, CellTypist, popV, FR-Match, Pan-Human Azimuth), four sc-proteomics CTann tools (DeepCell Types, DeepCell Types-HuBMAP, Robust Image-Based Cell Annotator [RIBCA], and SpaTial cELl LeARning [STELLAR]), plus a Cell Distance Explorer (CDE) Spatial Omics collection covering previously published annotations across 12 tissue types with 47,349,496 cells. Assigned cell types differ in number, resolution, and coverage. This paper details how 10 crosswalks were constructed, validated, and used to compile a "Supertree" that can be used to compare CTann across organs and technologies in support of reference atlas constitution and usage. All data and code can be accessed at https://cns-iu.github.io/hra-ctann-supporting-information.