Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

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

Abstract

The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.

Authors

  • Sebastian Köhler
    School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, National Institute of Informatics, Hitotsubashi, Tokyo, Japan, Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, Genetic Services of Western Australia, King Edward Memorial Hospital, WA 6008, Australia, School of Paediatrics and Child Health, University of Western Australia, WA 6008, Australia, Institute for Immunology and Infectious Diseases, Murdoch University, WA 6150, Australia, Office of Population Health, Public Health and Clinical Services Division, Western Australian Department of Health, WA 6004, Australia, Academic Department of Medical Genetics, Sydney Children's Hospitals Network (Westmead), NSW 2145, Australia, Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, NSW 2006, Australia, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany and Berlin Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany.
  • Leigh Carmody
    Monarch Initiative, monarchinitiative.org.
  • Nicole Vasilevsky
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • Julius O B Jacobsen
    Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
  • Daniel Danis
    Monarch Initiative, monarchinitiative.org.
  • Jean-Philippe Gourdine
    Monarch Initiative, monarchinitiative.org.
  • Michael Gargano
    Monarch Initiative, monarchinitiative.org.
  • Nomi L Harris
    Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.
  • Nicolas Matentzoglu
    School of Computer Science, University of Manchester, Oxford Road, Manchester, UK. nicolas.matentzoglu@manchester.ac.uk.
  • Julie A McMurry
    Monarch Initiative, monarchinitiative.org.
  • David Osumi-Sutherland
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
  • Valentina Cipriani
    UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.
  • James P Balhoff
    National Evolutionary Synthesis Center, Durham, NC 27705, USA; University of North Carolina, Chapel Hill, NC 27599, USA;
  • Tom Conlin
    Monarch Initiative, monarchinitiative.org.
  • Hannah Blau
    Monarch Initiative, monarchinitiative.org.
  • Gareth Baynam
    School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, National Institute of Informatics, Hitotsubashi, Tokyo, Japan, Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, Genetic Services of Western Australia, King Edward Memorial Hospital, WA 6008, Australia, School of Paediatrics and Child Health, University of Western Australia, WA 6008, Australia, Institute for Immunology and Infectious Diseases, Murdoch University, WA 6150, Australia, Office of Population Health, Public Health and Clinical Services Division, Western Australian Department of Health, WA 6004, Australia, Academic Department of Medical Genetics, Sydney Children's Hospitals Network (Westmead), NSW 2145, Australia, Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, NSW 2006, Australia, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany and Berlin Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, National Institute of Informatics, Hitotsubashi, Tokyo, Japan, Mouse Informa
  • Richard Palmer
    Spatial Sciences, Department of Science and Engineering, Curtin University, Perth, WA, Australia.
  • Dylan Gratian
    Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Department of Health, Government of Western Australia, WA, Australia.
  • Hugh Dawkins
    The Office of Population Health Genomics, Department of Health, Government of Western Australia, Perth, WA, Australia.
  • Michael Segal
    SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA.
  • Anna C Jansen
    Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium.
  • Ahmed Muaz
    Monarch Initiative, monarchinitiative.org.
  • Willie H Chang
    Centre for Computational Medicine, Hospital for Sick Children and Department of Computer Science, University of Toronto, Toronto, Canada.
  • Jenna Bergerson
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Stanley J F Laulederkind
    Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI53226, USA.
  • Zafer Yüksel
    Bioscientia GmbH, Ingelheim, Germany.
  • Sergi Beltran
    CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.
  • Alexandra F Freeman
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Panagiotis I Sergouniotis
    Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK.
  • Daniel Durkin
    The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
  • Andrea L Storm
    ICF, Rockville, MD, USA.
  • Marc Hanauer
    INSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
  • Michael Brudno
    Transplant AI Initiative, Ajmera Transplant Program, University Health Network, Toronto, ON, Canada.
  • Susan M Bello
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
  • Murat Sincan
  • Kayli Rageth
    Sanford Imagenetics, Sanford Health, Sioux Falls, SD, USA.
  • Matthew T Wheeler
    Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.
  • Renske Oegema
    Department of Genetics, University Medical Center Utrecht, the Netherlands.
  • Halima Lourghi
    INSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
  • Maria G Della Rocca
    ICF, Rockville, MD, USA.
  • Rachel Thompson
    John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
  • Francisco Castellanos
    The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
  • James Priest
    Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
  • Charlotte Cunningham-Rundles
    Division of Clinical Immunology, Icahn School of Medicine, Departments of Medicine and Pediatrics, Mount Sinai School of Medicine, New York, NY, United States.
  • Ayushi Hegde
    The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
  • Ruth C Lovering
    Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK. r.lovering@ucl.ac.uk.
  • Catherine Hajek
    Sanford Imagenetics, Sanford Health, Sioux Falls, SD, USA.
  • Annie Olry
    Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
  • Luigi Notarangelo
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Morgan Similuk
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Xingmin A Zhang
    Monarch Initiative, monarchinitiative.org.
  • David Gómez-Andrés
    Child Neurology Unit. Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.
  • Hanns Lochmüller
    John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
  • Hélène Dollfus
    Centre for Rare Eye Diseases CARGO, SENSGENE FSMR Network, Strasbourg University Hospital, Strasbourg, France. dollfus@unistra.fr.
  • Sergio Rosenzweig
    Immunology Service, Department of Laboratory Medicine, NIH Clinical Center, Bethesda, MD, USA.
  • Shruti Marwaha
    Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.
  • Ana Rath
    Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
  • Kathleen Sullivan
    Department of Pediatrics, Division of Allergy Immunology, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA.
  • Cynthia Smith
    The Jackson Laboratory, Bar Harbor, ME, USA.
  • Joshua D Milner
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Dorothée Leroux
    Centre for Rare Eye Diseases CARGO, SENSGENE FSMR Network, Strasbourg University Hospital, Strasbourg, France.
  • Cornelius F Boerkoel
    Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA.
  • Amy Klion
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Melody C Carter
    National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
  • Tudor Groza
    The Garvan Institute of Medical Research, Sydney, Australia.
  • Damian Smedley
    School of ITEE, The University of Queensland, St. Lucia, QLD 4072, Australia, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, National Institute of Informatics, Hitotsubashi, Tokyo, Japan, Mouse Informatics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, Genetic Services of Western Australia, King Edward Memorial Hospital, WA 6008, Australia, School of Paediatrics and Child Health, University of Western Australia, WA 6008, Australia, Institute for Immunology and Infectious Diseases, Murdoch University, WA 6150, Australia, Office of Population Health, Public Health and Clinical Services Division, Western Australian Department of Health, WA 6004, Australia, Academic Department of Medical Genetics, Sydney Children's Hospitals Network (Westmead), NSW 2145, Australia, Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, NSW 2006, Australia, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany and Berlin Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany.
  • Melissa A Haendel
    Library, Oregon Health & Science University, Portland, OR 97239, USA.
  • Chris Mungall
    Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Peter N Robinson
    The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA.

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