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PMID: 27899602 Published · ppublish English Journal Article Review

The Human Phenotype Ontology in 2017.

Nucleic acids research ·Vol. 45 ·No. D1 ·2017-00-04 ·Pages D865-D876

Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN

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.

MeSH Terms
Algorithms Biological Ontologies Computational Biology/methods Genetic Association Studies/methods Genomics/methods Humans Phenotype Precision Medicine/methods Rare Diseases/diagnosis,etiology Software Translational Research, Biomedical/methods
Authors & Affiliations
59 authors, click to expand affiliations / ORCID
Köhler Sebastian
Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany [email protected].
Vasilevsky Nicole A ORCID
Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Engelstad Mark
Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Foster Erin
Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
McMurry Julie
Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Aymé Ségolène
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.
Baynam Gareth
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.
Bello Susan M
The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
Boerkoel Cornelius F
Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA.
Boycott Kym M
Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
Brudno Michael
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.
Buske Orion J
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.
Chinnery Patrick F
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.
Cipriani Valentina
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.
Connell Laureen E
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
Dawkins Hugh J S
Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia.
DeMare Laura E
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
Devereau Andrew D
Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
de Vries Bert B A
Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands.
Firth Helen V
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Freson Kathleen
Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
Greene Daniel
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.
Hamosh Ada
McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Helbig Ingo
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.
Hum Courtney
Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada.
Jähn Johanna A
Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.
James Roger
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.
Krause Roland
LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
F Laulederkind Stanley J ORCID
Human and Molecular Genetics Center, Medical College of Wisconsin, USA.
Lochmüller Hanns
John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Lyon Gholson J
Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA.
Ogishima Soichi
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.
Olry Annie
Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
Ouwehand Willem H
Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
Pontikos Nikolas
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.
Rath Ana
Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
Schaefer Franz
Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany.
Scott Richard H
Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
Segal Michael
SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA.
Sergouniotis Panagiotis I
Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK.
Sever Richard
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
Smith Cynthia L
The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
Straub Volker
John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Thompson Rachel
John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Turner Catherine
John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Turro Ernest
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.
Veltman Marijcke W M
NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
Vulliamy Tom
Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
Yu Jing
Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK.
von Ziegenweidt Julie
Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
Zankl Andreas
Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia. | Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia.
Züchner Stephan
JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.
Zemojtel Tomasz
Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
Jacobsen Julius O B
Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
Groza Tudor
Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia. | St Vincent's Clinical School, Faculty of Medicine, UNSW Australia.
Smedley Damian
Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
Mungall Christopher J
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Haendel Melissa
Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Robinson Peter N
The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA [email protected]. | Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkw1039
Email
[email protected]
[email protected]
Published
2017-00-04
Epub
2016-00-28
Pages
D865-D876
Language
English
Region
England
NLM ID
0411011
PMCID
PMC5210535
Subset
IM
Grants
NHGRI NIH HHS · U01 HG009453 · United States
Department of Health · RP-PG-0310-1002 · United Kingdom
Medical Research Council · MC_UP_1501/2 · United Kingdom
NHGRI NIH HHS · U41 HG000330 · United States
NIH HHS · R24 OD011883 · United States
Medical Research Council · G1002274 · United Kingdom
British Heart Foundation · RG/09/012/28096 · United Kingdom
External Links
PubMed source DOI: 10.1093/nar/gkw1039 PMC Full Text View journal details
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