The Human Phenotype Ontology in 2017.

Journal: Nucleic acids research
Published Date: Nov 28, 2016

Abstract

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

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.
  • Nicole A Vasilevsky
    Ontology Development Group, Library, Oregon Health and Science University, Portland, Oregon, 97239, USA.
  • Mark Engelstad
    Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
  • Erin Foster
    Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
  • Julie McMurry
    Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
  • Ségolène Aymé
    Institut du Cerveau et de la Moelle épinière-ICM, CNRS UMR 7225-Inserm U 1127-UPMC-P6 UMR S 1127, Hôpital Pitié-Salpêtrière, 47, bd de l'Hôpital, 75013 Paris, France.
  • 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
  • Susan M Bello
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
  • Cornelius F Boerkoel
    Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA.
  • Kym M Boycott
    Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
  • Michael Brudno
    Transplant AI Initiative, Ajmera Transplant Program, University Health Network, Toronto, ON, Canada.
  • Orion J Buske
    Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.
  • Patrick F Chinnery
    Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
  • Valentina Cipriani
    UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.
  • Laureen E Connell
    Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
  • Hugh J S Dawkins
    Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia.
  • Laura E DeMare
    Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
  • Andrew D Devereau
    Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
  • Bert B A de Vries
    Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands.
  • Helen V Firth
    Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
  • Kathleen Freson
    Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
  • Daniel Greene
    Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
  • Ada Hamosh
    McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
  • Ingo Helbig
    Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.
  • Courtney Hum
    Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada.
  • Johanna A Jähn
    Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.
  • Roger James
    NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
  • Roland Krause
    LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
  • Stanley J F Laulederkind
    Human and Molecular Genetics Center, Medical College of Wisconsin, USA.
  • Hanns Lochmüller
    John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
  • Gholson J Lyon
    Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA.
  • Soichi Ogishima
    Department of Bioclinical Inforamtics, Tohoku Medical Megabank Organization, Tohoku University 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan.
  • Annie Olry
    Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
  • Willem H Ouwehand
    Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
  • Nikolas Pontikos
    University College London Institute of Ophthalmology, London, UK n.pontikos@ucl.ac.uk.
  • Ana Rath
    Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
  • Franz Schaefer
    Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany.
  • Richard H Scott
    Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
  • Michael Segal
    SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA.
  • Panagiotis I Sergouniotis
    Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK.
  • Richard Sever
    Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
  • Cynthia L Smith
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
  • Volker Straub
    John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
  • Rachel Thompson
    John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
  • Catherine Turner
    John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
  • Ernest Turro
    Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
  • Marijcke W M Veltman
    NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
  • Tom Vulliamy
    Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
  • Jing Yu
    Department of Ultrasound, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
  • Julie von Ziegenweidt
    Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
  • Andreas Zankl
    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
  • Stephan Züchner
    JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.
  • Tomasz Zemojtel
    Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland.
  • Julius O B Jacobsen
    Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
  • 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.
  • Christopher J Mungall
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Melissa Haendel
    Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
  • Peter N Robinson
    The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA.

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