Human Disease Ontology 2018 update: classification, content and workflow expansion.

Journal: Nucleic acids research
Published Date: Jan 8, 2019

Abstract

The Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-inferred mechanistic disease classifications, thus providing novel perspectives on related diseases. Expansion of disease terms, alternative anatomy, cell type and genetic disease classifications and workflow automation highlight the updates for the DO since 2015. The enhanced breadth and depth of the DO's knowledgebase has expanded the DO's utility for exploring the multi-etiology of human disease, thus improving the capture and communication of health-related data across biomedical databases, bioinformatics tools, genomic and cancer resources and demonstrated by a 6.6× growth in DO's user community since 2015. The DO's continual integration of human disease knowledge, evidenced by the more than 200 SVN/GitHub releases/revisions, since previously reported in our DO 2015 NAR paper, includes the addition of 2650 new disease terms, a 30% increase of textual definitions, and an expanding suite of disease classification hierarchies constructed through defined logical axioms.

Authors

  • Lynn M Schriml
    Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC 20037, USA, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Center for Bioinformatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892-9760, USA, NASA Jet Propulsion Laboratory, Pasadena, CA, USA, Division of Cancer Prevention, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892-9760, USA, Wellcome Trust Sanger Institute, Cambridge, UK and McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA.
  • Elvira Mitraka
    Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC 20037, USA, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Center for Bioinformatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892-9760, USA, NASA Jet Propulsion Laboratory, Pasadena, CA, USA, Division of Cancer Prevention, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20892-9760, USA, Wellcome Trust Sanger Institute, Cambridge, UK and McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA.
  • James Munro
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
  • Becky Tauber
    University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.
  • Mike Schor
    University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.
  • Lance Nickle
    University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.
  • Victor Felix
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
  • Linda Jeng
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Cynthia Bearer
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Richard Lichenstein
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Katharine Bisordi
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Nicole Campion
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Brooke Hyman
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • David Kurland
    New York University Langone Medical Center, Department of Neurosurgery, New York, NY, USA.
  • Connor Patrick Oates
    Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Siobhan Kibbey
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Poorna Sreekumar
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Chris Le
    University of Maryland School of Medicine, Baltimore, MD, USA.
  • Michelle Giglio
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK.
  • Carol Greene
    University of Maryland School of Medicine, Baltimore, MD, USA.

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