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

Journal: BMC bioinformatics
PMID: 31272390

Abstract

BACKGROUND: 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+).

Authors

  • James A Overton
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • Randi Vita
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • Patrick Dunn
    ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA.
  • Julie G Burel
    Division for Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
  • Syed Ahmad Chan Bukhari
    Department of Pathology, Yale School of Medicine, New Haven, CT, USA. ahmad.chan@yale.edu.
  • Kei-Hoi Cheung
    Department of Emergency Medicine, Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT USA ; VA Connecticut Healthcare System, West Haven, CT USA ; Extracellular RNA Communication Consortium (ERCC), ᅟ, ᅟ
  • Steven H Kleinstein
    Department of Pathology, Yale School of Medicine, New Haven, CT, USA. steven.kleinstein@yale.edu.
  • Alexander D Diehl
    Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, J. Craig Venter Institute, La Jolla, CA 92037, USA, Department of Pathology, University of California, San Diego, CA 92093, USA.
  • Bjoern Peters
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.

Keywords

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