The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Journal: Journal of biomedical semantics
Published Date:

Abstract

BACKGROUND: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies.

Authors

  • 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.
  • Terrence F Meehan
    Samples, Phenotypes and Ontologies, European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, Cambridge UK.
  • Yvonne M Bradford
    ZFIN, the Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR, 97403, USA.
  • Matthew H Brush
    Oregon Health and Science University, Portland, Oregon, United States of America.
  • Wasila M Dahdul
    Department of Biology, University of South Dakota, Vermillion, SD, 57069, USA.
  • David S Dougall
    Southwestern Medical Center, University of Texas, Dallas, TX, 75235, USA.
  • 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.
  • David Osumi-Sutherland
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
  • Alan Ruttenberg
    School of Dental Medicine, State University of New York at Buffalo, Buffalo, New York, United States of America.
  • Sirarat Sarntivijai
    European Bioinformatics Institute (EMBL-EBI),European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
  • Ceri E Van Slyke
    ZFIN, the Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, OR, 97403, USA.
  • Nicole A Vasilevsky
    Ontology Development Group, Library, Oregon Health and Science University, Portland, Oregon, 97239, USA.
  • Melissa A Haendel
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • Judith A Blake
    The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.