CL: Cell Ontology

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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.

Cell type discovery and representation in the era of high-content single cell phenotyping.
BMC bioinformatics. 2017-12-21; 18.Suppl 17: 559.
PMID: 29322913
flowCL: ontology-based cell population labelling in flow cytometry.
Bioinformatics (Oxford, England). 2015-04-15; 31.8: 1337-9.
PMID: 25481008
Hematopoietic cell types: prototype for a revised cell ontology.
Journal of biomedical informatics. 2011-02-01; 44.1: 75-9.
PMID: 20123131
An improved ontological representation of dendritic cells as a paradigm for all cell types.
BMC bioinformatics. 2009-02-25; 10.70.
PMID: 19243617

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