title: The Human Phenotype Ontology in 2017.
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.affiliation: Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany dr.sebastian.koehler@gmail.com.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Köhler
authors.affiliation: Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Nicole A
authors.identifier: 0000-0001-5208-3432
authors.initials: NA
authors.lastname: Vasilevsky
authors.affiliation: Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Engelstad
authors.affiliation: Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Foster
authors.affiliation: Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Julie
authors.initials: J
authors.lastname: McMurry
authors.affiliation: 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.
authors.forename: Ségolène
authors.initials: S
authors.lastname: Aymé
authors.affiliation: Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital Department of Health, Government of Western Australia, Perth, WA 6008, Australia.|School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia.
authors.forename: Gareth
authors.initials: G
authors.lastname: Baynam
authors.affiliation: The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Bello
authors.affiliation: Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA.
authors.forename: Cornelius F
authors.initials: CF
authors.lastname: Boerkoel
authors.affiliation: Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
authors.forename: Kym M
authors.initials: KM
authors.lastname: Boycott
authors.affiliation: 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.
authors.forename: Michael
authors.initials: M
authors.lastname: Brudno
authors.affiliation: 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.
authors.forename: Orion J
authors.initials: OJ
authors.lastname: Buske
authors.affiliation: Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.|NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
authors.forename: Patrick F
authors.initials: PF
authors.lastname: Chinnery
authors.affiliation: UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.|UCL Genetics Institute, University College London, London WC1E 6BT, UK.
authors.forename: Valentina
authors.initials: V
authors.lastname: Cipriani
authors.affiliation: Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
authors.forename: Laureen E
authors.initials: LE
authors.lastname: Connell
authors.affiliation: Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia.
authors.forename: Hugh J S
authors.initials: HJ
authors.lastname: Dawkins
authors.affiliation: Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
authors.forename: Laura E
authors.initials: LE
authors.lastname: DeMare
authors.affiliation: Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Devereau
authors.affiliation: Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Bert B A
authors.initials: BB
authors.lastname: de Vries
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: Helen V
authors.initials: HV
authors.lastname: Firth
authors.affiliation: Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Freson
authors.affiliation: Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.|Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
authors.forename: Daniel
authors.initials: D
authors.lastname: Greene
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
authors.forename: Ada
authors.initials: A
authors.lastname: Hamosh
authors.affiliation: Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.|Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.
authors.forename: Ingo
authors.initials: I
authors.lastname: Helbig
authors.affiliation: Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada.
authors.forename: Courtney
authors.initials: C
authors.lastname: Hum
authors.affiliation: Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.
authors.forename: Johanna A
authors.initials: JA
authors.lastname: Jähn
authors.affiliation: NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.|Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
authors.forename: Roger
authors.initials: R
authors.lastname: James
authors.affiliation: LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
authors.forename: Roland
authors.initials: R
authors.lastname: Krause
authors.affiliation: Human and Molecular Genetics Center, Medical College of Wisconsin, USA.
authors.forename: Stanley J
authors.identifier: 0000-0001-5356-4174
authors.initials: SJ
authors.lastname: F Laulederkind
authors.affiliation: John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
authors.forename: Hanns
authors.initials: H
authors.lastname: Lochmüller
authors.affiliation: Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA.
authors.forename: Gholson J
authors.initials: GJ
authors.lastname: Lyon
authors.affiliation: Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Tohoku Medical Megabank Organization Bldg 7F room #741,736, Seiryo 2-1, Aoba-ku, Sendai Miyagi 980-8573 Japan.
authors.forename: Soichi
authors.initials: S
authors.lastname: Ogishima
authors.affiliation: Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
authors.forename: Annie
authors.initials: A
authors.lastname: Olry
authors.affiliation: Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
authors.forename: Willem H
authors.initials: WH
authors.lastname: Ouwehand
authors.affiliation: UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.|UCL Genetics Institute, University College London, London WC1E 6BT, UK.
authors.forename: Nikolas
authors.initials: N
authors.lastname: Pontikos
authors.affiliation: Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
authors.forename: Ana
authors.initials: A
authors.lastname: Rath
authors.affiliation: Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany.
authors.forename: Franz
authors.initials: F
authors.lastname: Schaefer
authors.affiliation: Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Scott
authors.affiliation: SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Segal
authors.affiliation: Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK.
authors.forename: Panagiotis I
authors.initials: PI
authors.lastname: Sergouniotis
authors.affiliation: Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Sever
authors.affiliation: The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
authors.forename: Cynthia L
authors.initials: CL
authors.lastname: Smith
authors.affiliation: John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
authors.forename: Volker
authors.initials: V
authors.lastname: Straub
authors.affiliation: John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
authors.forename: Rachel
authors.initials: R
authors.lastname: Thompson
authors.affiliation: John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
authors.forename: Catherine
authors.initials: C
authors.lastname: Turner
authors.affiliation: Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.|Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
authors.forename: Ernest
authors.initials: E
authors.lastname: Turro
authors.affiliation: NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
authors.forename: Marijcke W M
authors.initials: MW
authors.lastname: Veltman
authors.affiliation: Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
authors.forename: Tom
authors.initials: T
authors.lastname: Vulliamy
authors.affiliation: Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK.
authors.forename: Jing
authors.initials: J
authors.lastname: Yu
authors.affiliation: Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
authors.forename: Julie
authors.initials: J
authors.lastname: von Ziegenweidt
authors.affiliation: Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.|Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia.
authors.forename: Andreas
authors.initials: A
authors.lastname: Zankl
authors.affiliation: JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.
authors.forename: Stephan
authors.initials: S
authors.lastname: Züchner
authors.affiliation: Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Zemojtel
authors.affiliation: Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
authors.forename: Julius O B
authors.initials: JO
authors.lastname: Jacobsen
authors.affiliation: Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.|St Vincent's Clinical School, Faculty of Medicine, UNSW Australia.
authors.forename: Tudor
authors.initials: T
authors.lastname: Groza
authors.affiliation: Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
authors.forename: Damian
authors.initials: D
authors.lastname: Smedley
authors.affiliation: Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.affiliation: Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Haendel
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA peter.robinson@jax.org.|Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Robinson
mesh_terms: D000465:Algorithms; D064229:Biological Ontologies; D019295:Computational Biology / Q000379:methods; D056726:Genetic Association Studies / Q000379:methods; D023281:Genomics / Q000379:methods; D006801:Humans; D010641:Phenotype; D057285:Precision Medicine / Q000379:methods; D035583:Rare Diseases / Q000175:diagnosis / Q000209:etiology; D012984:Software; D057170:Translational Research, Biomedical / Q000379:methods