This crosswalk maps the cell type annotations from Azimuth (Hao et al. 2021) to Cell Ontology Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-04-10/cl.owl. More information on Azimuth is available at https://azimuth.hubmapconsortium.org/.

The Human Reference Atlas regularly adds new cell types to Cell Ontology; an overview and current numbers are available under "Ontologies Extended" at https://apps.humanatlas.io/dashboard/data.

Bibliography:

• Hao, Yuhan, Stephanie Hao, Erica Andersen-Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Maddie J. Lee, et al. 2021. “Integrated Analysis of Multimodal Single-Cell Data.” Cell 184 (13): 3573-3587.e29. https://doi.org/10.1016/j.cell.2021.04.048.

This dataset contains the cell-type annotations of each scRNA-seq dataset that was used in the omnideconv benchmarking study. We do not include the count matrix files in here, they will have to be accessed from the original publications and are linked here.Each annotation file includes a table with columns for the cell barcode and their annotation, with different granularity of annotation, if available. Included datasets (and their accession codes) are:Hao (GSE164378): Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021)Maynard (PRJNA591860): Maynard, A. et al. Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing. Cell 182, 1232–1251.e22 (2020)Lambrechts (E-MTAB-6149, E-MTAB-6653): Lambrechts, D. et al. Phenotype molding of stromal cells in the lung tumor microenvironment. Nat. Med. 24, 1277–1289 (2018) Tabula-Muris (GSE109774): Tabula Muris Consortium et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 562, 367–372 (2018)Wu (GSE176078): Wu, S. Z. et al. A single-cell and spatially resolved atlas of human breast cancers. Nat. Genet. 53, 1334–1347 (2021)