CL: Cell Ontology

A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal functioning of different organs and tissues, they can also be used as cellular biomarkers of a variety of different disease states and therapeutic/vaccine responses.

In order to serve as a reference for cell type representation, the Cell Ontology has been developed to provide a standard nomenclature of defined cell types for comparative analysis and biomarker discovery. Historically, these cell types have been defined based on unique cellular shapes and structures, anatomic locations, and marker protein expression. However, we are now experiencing a revolution in cellular characterization resulting from the application of new high-throughput, high-content cytometry and sequencing technologies.

The resulting explosion in the number of distinct cell types being identified is challenging the current paradigm for cell type definition in the Cell Ontology. In this project, we are exploring examples of state-of-the-art cellular biomarker characterization using high-content cytometry and single cell RNA sequencing, and determining strategies for standardized cell type representations based on the data outputs from these cutting-edge technologies.


BMC bioinformatics. 2017-12-21; 18.Suppl 17: 559.
Cell type discovery and representation in the era of high-content single cell phenotyping
Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH
PMID: 29322913
Bioinformatics (Oxford, England). 2015-04-15; 31.8: 1337-9.
flowCL: ontology-based cell population labelling in flow cytometry
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR
PMID: 25481008
Journal of biomedical informatics. 2011-02-01; 44.1: 75-9.
Hematopoietic cell types: prototype for a revised cell ontology
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ
PMID: 20123131
BMC bioinformatics. 2009-02-25; 10.70.
An improved ontological representation of dendritic cells as a paradigm for all cell types
Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG
PMID: 19243617


This work is funded by the Chan Zuckerberg Initiative DAF under grant no. 2018-182730.

Principal Investigator

Key Staff

  • Brian Aevermann, MS


Alexander D. Diehl
University of Buffalo

David Osumi-Sutherland
European Bioinformatics Institute

Lindsay Cowell
University of Texas Southwestern Medical Center

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