Nicole Vasilevsky1,2*, Aleix Puig-Barbe3*, Andreas Bueckle1, Ellen M. Quardokus1, Yongxin Kong1, Divya Prasanth Paraman1, Jie Zheng4, Yongqun He4, Yashvardhan Jain1, Bruce W. Herr II1, Katy Börner1*
1 Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
2 Rose City Data Science, Portland, OR, USA
3 European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
4 University of Michigan Medical School, Ann Arbor, MI, USA
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://github.com/cns-iu/hra-ctann-supporting-information.
The repo is structured in the following way:
├── code
├── data
├── docs
├── supertree
The code folder contains the scripts and notebooks used to generate the manuscript figures and tables, as well as the source code for the interactive Supertree visualization.
The data folder contains the supertree raw data spreadsheet.
The docs folder contains generated static files published through GitHub Pages. These files are build outputs and should not be edited directly. Note that the Supertree source code and build instructions are located in code/supertree/. Running the build script generates the published site under docs/supertree/.
The supertree folder contains the files to create the supertree visualization.
The following Digital Objects are described in this paper and are available at the link below:
Azimuth: https://purl.humanatlas.io/ctann/azimuth/v1.4
CellTypist: https://purl.humanatlas.io/ctann/celltypist/v1.3
DeepCell Types: https://purl.humanatlas.io/ctann/deepcelltypes/v1.2
DeepCell Types-HuBMAP: https://purl.humanatlas.io/ctann/deepcelltypes-hubmap/v1.2
FR-Match: https://purl.humanatlas.io/ctann/frmatch/v1.0
Pan-Human Azimuth: https://purl.humanatlas.io/ctann/pan-human-azimuth/v1.2
popV: https://purl.humanatlas.io/ctann/popv/v1.4
RIBCA: https://purl.humanatlas.io/ctann/ribca/v1.0
STELLAR: https://purl.humanatlas.io/ctann/stellar/v1.0
CDE Spatial Omics: https://purl.humanatlas.io/ctann/vccf/v1.2
The raw Supertree data is available here: https://github.com/cns-iu/hra-ctann-supporting-information/tree/main/data/CTann-Supertree-v10.csv. The list of excluded cells from the Suptertree is available here: https://github.com/cns-iu/hra-ctann-supporting-information/blob/main/data/CTann-Supertree-Excluded-Cells.csv.
The interactive Supertree can be found here. The Supertree source code and usage instructions are in the /supertree directory.