{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T21:32:27Z","timestamp":1768339947878,"version":"3.49.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Finding one or more cell populations of interest, such as those correlating to a specific disease, is critical when analysing flow cytometry data. However, labelling of cell populations is not well defined, making it difficult to integrate the output of algorithms to external knowledge sources.<\/jats:p>\n               <jats:p>Results: We developed flowCL, a software package that performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case.<\/jats:p>\n               <jats:p>Conclusion: By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproducible identification of standardized cell types.<\/jats:p>\n               <jats:p>Availability and implementation: Code, R script and documentation are available under the Artistic 2.0 license through Bioconductor (http:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/flowCL.html).<\/jats:p>\n               <jats:p>Contact: \u00a0rbrinkman@bccrc.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu807","type":"journal-article","created":{"date-parts":[[2014,12,7]],"date-time":"2014-12-07T01:08:27Z","timestamp":1417914507000},"page":"1337-1339","source":"Crossref","is-referenced-by-count":20,"title":["flowCL: ontology-based cell population labelling in flow cytometry"],"prefix":"10.1093","volume":"31","author":[{"given":"M\u00e9lanie","family":"Courtot","sequence":"first","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin","family":"Meskas","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander D.","family":"Diehl","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Radina","family":"Droumeva","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raphael","family":"Gottardo","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrin","family":"Jalali","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad Jafar","family":"Taghiyar","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Holden T.","family":"Maecker","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J. Philip","family":"McCoy","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."},{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alan","family":"Ruttenberg","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard H.","family":"Scheuermann","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."},{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryan R.","family":"Brinkman","sequence":"additional","affiliation":[{"name":"1 Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, 2Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, 3Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, 4Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 5Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA, 6National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA, 7Center for Human Immunology, Autoimmunity and Inflammation, National Institutes of Health, Bethesda, MD 20892, USA, 8School of Dental Medicine, University at Buffalo, NY 14214-8006, USA, 9J. Craig Venter Institute, La Jolla, CA 92037, USA, 10Department of Pathology, University of California, San Diego, CA 92093, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,12,6]]},"reference":[{"key":"2023051309033436300_btu807-B1","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.jbi.2010.01.006","article-title":"Hematopoietic cell types: prototype for a revised cell ontology","volume":"44","author":"Diehl","year":"2011","journal-title":"J. Biomed. Inf."},{"key":"2023051309033436300_btu807-B2","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003806","article-title":"OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis","volume":"10","author":"Finak","year":"2014","journal-title":"PLoS Comput. 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