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Cell type ontologies of the Human Cell Atlas

Nature Cell Biology volume 23, pages 1129–1135 (2021)Cite this article

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Abstract

Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body while at the same time raising the need to formalize this new knowledge. Here, we discuss current efforts to harmonize and integrate different sources of annotations of cell types and states into a reference cell ontology. We illustrate with examples how a unified ontology can consolidate and advance our understanding of cell types across scientific communities and biological domains.

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Fig. 1: Representation of part of CL centred around the term Kupffer cell.
Fig. 2: CL links human cell types with anatomy and cell-state transition.

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Acknowledgements

We are grateful to J. Eliasova (scientific illustrator) for support with the figure, to R. Vento-Tormo for comments on the figure and texts, and to the following clinicians and researchers for information on standard pathology markers for tissues and cells: L. Campos, A. Dean, L. Moore, N. Sebire, T. Brevini, M. Haniffa, J. E. Kwa, J. McCaffrey and A. Kreins. We also thank all members of the CL and Uberon editorial teams, including C. Mungall, N. Matentzoglu, A. Diehl, N. Washington, S. Tan, P. Roncaglia, T. Lubiana and D. Goutte-Gattat. Research reported in this publication was supported by the Wellcome Trust (grant 108413/A/15/D), the Office of the Director, National Institutes of Health of the National Institutes of Health (under award number OT2OD026682’), grants from the CZI (Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation), and Schmidt Futures (Grant 74). This publication is part of the HCA (www.humancellatlas.org/publications/).

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Authors and Affiliations

  1. EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK

    David Osumi-Sutherland

  2. Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK

    Chuan Xu, Maria Keays & Sarah A. Teichmann

  3. Research Department of Pathology, University College London, London, UK

    Adam P. Levine

  4. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

    Peter V. Kharchenko

  5. Genentech, South San Francisco, CA, USA

    Aviv Regev

  6. Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Aviv Regev

  7. Allen Institute for Brain Science, Seattle, WA, USA

    Ed Lein

  8. Cavendish Laboratory, University of Cambridge, Cambridge, UK

    Sarah A. Teichmann

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  1. David Osumi-Sutherland
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Correspondence to Sarah A. Teichmann.

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Competing interests

Since January 2019, S.A.T. has been remunerated for consulting and SAB membership by Foresite Labs, GlaxoSmithKline, Biogen, Roche and Genentech, and is a founder and equity holder of Transition Bio. A.R. is a cofounder and equity holder in Celsius Therapeutics, an equity holder in Immunitas Therapeutics, and was a scientific advisory board member for ThermoFisher Scientific, Asimov, Syros Pharmaceuticals and Neogene Therapeutics until 31 July 2020. From 1 August 2020, A.R. is an employee of Genentech, a member of the Roche group. A.R. is a named inventor on several patents and patent applications filed by the Broad Institute in the area of single-cell and spatial genomics. The other authors declare no competing interests.

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Osumi-Sutherland, D., Xu, C., Keays, M. et al. Cell type ontologies of the Human Cell Atlas. Nat Cell Biol 23, 1129–1135 (2021). https://doi.org/10.1038/s41556-021-00787-7

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