Reporting and connecting cell type names and gating definitions through ontologies
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...
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doaj-143a76f8dbf943c198ef9fadd6d456bd2020-11-25T03:02:43ZengBMCBMC Bioinformatics1471-21052019-04-0120S525926410.1186/s12859-019-2725-5Reporting and connecting cell type names and gating definitions through ontologiesJames A. Overton0Randi Vita1Patrick Dunn2Julie G. Burel3Syed Ahmad Chan Bukhari4Kei-Hoi Cheung5Steven H. Kleinstein6Alexander D. Diehl7Bjoern Peters8Knocean Inc.Division for Vaccine Discovery, La Jolla Institute for Allergy and ImmunologyImmPort Curation Team, NG Health SolutionsDivision for Vaccine Discovery, La Jolla Institute for Allergy and ImmunologyDepartment of Pathology, Yale School of MedicineDepartment of Emergency Medicine and Yale Center for Medical Informatics, Yale School of MedicineDepartment of Pathology, Yale School of MedicineDepartment of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at BuffaloDivision for Vaccine Discovery, La Jolla Institute for Allergy and ImmunologyAbstract 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+). Results 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. Conclusions 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.http://link.springer.com/article/10.1186/s12859-019-2725-5Cell typeStandardsGating definitionsHuman immunology project consortiumImmunology database and analysis portal protein ontologyCell ontology |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
James A. Overton Randi Vita Patrick Dunn Julie G. Burel Syed Ahmad Chan Bukhari Kei-Hoi Cheung Steven H. Kleinstein Alexander D. Diehl Bjoern Peters |
spellingShingle |
James A. Overton Randi Vita Patrick Dunn Julie G. Burel Syed Ahmad Chan Bukhari Kei-Hoi Cheung Steven H. Kleinstein Alexander D. Diehl Bjoern Peters Reporting and connecting cell type names and gating definitions through ontologies BMC Bioinformatics Cell type Standards Gating definitions Human immunology project consortium Immunology database and analysis portal protein ontology Cell ontology |
author_facet |
James A. Overton Randi Vita Patrick Dunn Julie G. Burel Syed Ahmad Chan Bukhari Kei-Hoi Cheung Steven H. Kleinstein Alexander D. Diehl Bjoern Peters |
author_sort |
James A. Overton |
title |
Reporting and connecting cell type names and gating definitions through ontologies |
title_short |
Reporting and connecting cell type names and gating definitions through ontologies |
title_full |
Reporting and connecting cell type names and gating definitions through ontologies |
title_fullStr |
Reporting and connecting cell type names and gating definitions through ontologies |
title_full_unstemmed |
Reporting and connecting cell type names and gating definitions through ontologies |
title_sort |
reporting and connecting cell type names and gating definitions through ontologies |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2019-04-01 |
description |
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+). Results 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. Conclusions 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. |
topic |
Cell type Standards Gating definitions Human immunology project consortium Immunology database and analysis portal protein ontology Cell ontology |
url |
http://link.springer.com/article/10.1186/s12859-019-2725-5 |
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