OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.

Journal: BMC bioinformatics
Published Date:

Abstract

BACKGROUND: Stem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respectively.

Authors

  • Yongqun He
    University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.
  • William D Duncan
    Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
  • Daniel J Cooper
    University of Miami, Miami, FL, USA.
  • Jens Hansen
    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
  • Ravi Iyengar
    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA. Ravi.Iyengar@mssm.edu.
  • Edison Ong
    University of Michigan Medical School, Ann Arbor, MI 48109, USA.
  • Kendal Walker
    University of Michigan Medical School, Ann Arbor, MI, USA.
  • Omar Tibi
    John Hopkins Unversity, Baltimore, MD, USA.
  • Sam Smith
  • Lucas M Serra
    Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
  • Jie Zheng
    State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China.
  • Sirarat Sarntivijai
    European Bioinformatics Institute (EMBL-EBI),European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Stephan Schürer
    Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA. sschurer@med.miami.edu.
  • K Sue O'Shea
    University of Michigan Medical School, Ann Arbor, MI, USA.
  • 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.