The Human Phenotype Ontology in 2017

Sebastian Köhler¹, Nicole A Vasilevsky², Mark Engelstad², Erin Foster², Julie McMurry², Ségolène Aymé³, Gareth Baynam^{4

5}, Susan M Bello⁶, Cornelius F Boerkoel⁷, Kym M Boycott⁸, Michael Brudno⁹, Orion J Buske⁹, Patrick F Chinnery^{10

11}, Valentina Cipriani^{12

13}, Laureen E Connell¹⁴, Hugh J S Dawkins¹⁵, Laura E DeMare¹⁴, Andrew D Devereau¹⁶, Bert B A de Vries¹⁷, Helen V Firth¹⁸, Kathleen Freson¹⁹, Daniel Greene^{20

21}, Ada Hamosh²², Ingo Helbig^{23

24}, Courtney Hum²⁵, Johanna A Jähn²⁴, Roger James^{11

21}, Roland Krause²⁶, Stanley J F Laulederkind²⁷, Hanns Lochmüller²⁸, Gholson J Lyon²⁹, Soichi Ogishima³⁰, Annie Olry³¹, Willem H Ouwehand²¹, Nikolas Pontikos^{12

13}, Ana Rath³¹, Franz Schaefer³², Richard H Scott¹⁶, Michael Segal³³, Panagiotis I Sergouniotis³⁴, Richard Sever¹⁴, Cynthia L Smith⁶, Volker Straub²⁸, Rachel Thompson²⁸, Catherine Turner²⁸, Ernest Turro^{20

21}, Marijcke W M Veltman¹¹, Tom Vulliamy³⁵, Jing Yu³⁶, Julie von Ziegenweidt²⁰, Andreas Zankl^{37

38}, Stephan Züchner³⁹, Tomasz Zemojtel⁴⁰, Julius O B Jacobsen¹⁶, Tudor Groza^{41

42}, Damian Smedley¹⁶, Christopher J Mungall⁴³, Melissa Haendel², Peter N Robinson^{44

45}

Affiliations

¹ Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany dr.sebastian.koehler@gmail.com.
² Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
³ 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.
⁴ 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.
⁵ School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia.
⁶ The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
⁷ Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA.
⁸ Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
⁹ 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.
¹⁰ Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
¹¹ NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
¹² UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.
¹³ UCL Genetics Institute, University College London, London WC1E 6BT, UK.
¹⁴ Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
¹⁵ Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia.
¹⁶ Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
¹⁷ Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands.
¹⁸ Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
¹⁹ Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
²⁰ Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
²¹ Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
²² McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
²³ Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.
²⁴ Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.
²⁵ Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada.
²⁶ LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
²⁷ Human and Molecular Genetics Center, Medical College of Wisconsin, USA.
²⁸ John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
²⁹ Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA.
³⁰ 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.
³¹ Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
³² Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany.
³³ SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA.
³⁴ Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK.
³⁵ Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
³⁶ Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK.
³⁷ Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.
³⁸ Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia.
³⁹ JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.
⁴⁰ Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
⁴¹ Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.
⁴² St Vincent's Clinical School, Faculty of Medicine, UNSW Australia.
⁴³ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
⁴⁴ The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA peter.robinson@jax.org.
⁴⁵ Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.

PMID: 27899602
PMCID: PMC5210535
DOI: 10.1093/nar/gkw1039

Review

The Human Phenotype Ontology in 2017

Sebastian Köhler et al. Nucleic Acids Res. 2017.

. 2017 Jan 4;45(D1):D865-D876.

doi: 10.1093/nar/gkw1039. Epub 2016 Nov 28.

Authors

Affiliations

¹ Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany dr.sebastian.koehler@gmail.com.
² Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
³ 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.
⁴ 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.
⁵ School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia.
⁶ The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
⁷ Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA.
⁸ Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
⁹ 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.
¹⁰ Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
¹¹ NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
¹² UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.
¹³ UCL Genetics Institute, University College London, London WC1E 6BT, UK.
¹⁴ Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
¹⁵ Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia.
¹⁶ Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
¹⁷ Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands.
¹⁸ Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
¹⁹ Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
²⁰ Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
²¹ Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
²² McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
²³ Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.
²⁴ Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.
²⁵ Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada.
²⁶ LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
²⁷ Human and Molecular Genetics Center, Medical College of Wisconsin, USA.
²⁸ John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
²⁹ Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA.
³⁰ 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.
³¹ Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
³² Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany.
³³ SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA.
³⁴ Manchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK.
³⁵ Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
³⁶ Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK.
³⁷ Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.
³⁸ Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia.
³⁹ JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.
⁴⁰ Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
⁴¹ Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.
⁴² St Vincent's Clinical School, Faculty of Medicine, UNSW Australia.
⁴³ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
⁴⁴ The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA peter.robinson@jax.org.
⁴⁵ Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.

PMID: 27899602
PMCID: PMC5210535
DOI: 10.1093/nar/gkw1039

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.

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Figures

**Figure 1.**
Distribution of HPO class additions per general category of phenotypic abnormalities. The figure shows the number of terms added per category since the previous Nucleic Acids Research database article in 2014 (8).

See this image and copyright information in PMC

References

1. Robinson P.N., Köhler S., Bauer S., Seelow D., Horn D., Mundlos S. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet. 2008;83:610–615. - PMC - PubMed
1. McMurry J.A., Köhler S., Washington N.L., Balhoff J.P., Borromeo C., Brush M., Carbon S., Conlin T., Dunn N., Engelstad M., et al. Navigating the phenotype frontier: the monarch initiative. Genetics. 2016;203:1491–1495. - PMC - PubMed
1. Rath A., Olry A., Dhombres F., Brandt M.M.C., Urbero B., Ayme S. Representation of rare diseases in health information systems: the Orphanet approach to serve a wide range of end users. Hum. Mutat. 2012;33:803–808. - PubMed
1. Biesecker L.G. Phenotype matters. Nat. Genet. 2004;36:323–324. - PubMed
1. Robinson P.N., Webber C. Phenotype ontologies and cross-species analysis for translational research. PLoS Genet. 2014;10:e1004268. - PMC - PubMed

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The Human Phenotype Ontology in 2017

Affiliations

The Human Phenotype Ontology in 2017

Authors

Affiliations

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources