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BMC Bioinformatics. 2019 Apr 25;20(Suppl 5):182. doi: 10.1186/s12859-019-2725-5.

Reporting and connecting cell type names and gating definitions through ontologies.

Author information

Knocean Inc., Toronto, Ontario, Canada.
Division for Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA.
Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA.
Department of Emergency Medicine and Yale Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA.
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
Division for Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
Department of Medicine, University of California San Diego, La Jolla, CA, USA.



Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations based on the detection of a pattern of markers. The description of the cell populations targeted in such experiments typically have two complementary components: the description of the cell type targeted (e.g. 'T cells'), and the description of the marker pattern utilized (e.g. CD14-, CD3+).


We here describe our attempts to use ontologies to cross-compare cell types and marker patterns (also referred to as gating definitions). We used a large set of such gating definitions and corresponding cell types submitted by different investigators into ImmPort, a central database for immunology studies, to examine the ability to parse gating definitions using terms from the Protein Ontology (PRO) and cell type descriptions, using the Cell Ontology (CL). We then used logical axioms from CL to detect discrepancies between the two.


We suggest adoption of our proposed format for describing gating and cell type definitions to make comparisons easier. We also suggest a number of new terms to describe gating definitions in flow cytometry that are not based on molecular markers captured in PRO, but on forward- and side-scatter of light during data acquisition, which is more appropriate to capture in the Ontology for Biomedical Investigations (OBI). Finally, our approach results in suggestions on what logical axioms and new cell types could be considered for addition to the Cell Ontology.


Cell ontology; Cell type; Gating definitions; HIPC; Human immunology project consortium; ImmPort; Immunology database and analysis portal protein ontology; Standards

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