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Nucleic Acids Res. 2019 Jan 8;47(D1):D1018-D1027. doi: 10.1093/nar/gky1105.

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

Author information

1
Charité Centrum für Therapieforschung, Charité-Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.
2
Einstein Center Digital Future, Berlin 10117, Germany.
3
Monarch Initiative, monarchinitiative.org.
4
The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
5
Oregon Health & Science University, Portland, OR 97217, USA.
6
Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
7
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
8
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
9
Linus Pauling institute, Oregon State University, Corvallis, OR, USA.
10
William Harvey Research Institute, Queen Mary University College of London.
11
UCL Genetics Institute, University College of London.
12
UCL Institute of Ophthalmology, University College of London.
13
Renaissance Computing Institute, University of North Carolina at Chapel Hill.
14
Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Department of Health, Government of Western Australia, WA, Australia.
15
School of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
16
Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.
17
Spatial Sciences, Department of Science and Engineering, Curtin University, Perth, WA, Australia.
18
The Office of Population Health Genomics, Department of Health, Government of Western Australia, Perth, WA, Australia.
19
SimulConsult, Chestnut Hill, MA, USA.
20
Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium.
21
Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Brussels, Belgium.
22
Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.
23
Centre for Computational Medicine, Hospital for Sick Children and Department of Computer Science, University of Toronto, Toronto, Canada.
24
National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
25
Rat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, 8701 Watertown Plank Road Milwaukee, WI 53226, USA.
26
Bioscientia GmbH, Ingelheim, Germany.
27
CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.
28
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
29
University of Manchester & Manchester Royal Eye Hospital, Manchester, UK.
30
ICF, Rockville, MD, USA.
31
National Center for Advancing Translational Sciences, Office of Rare Diseases Research, National Institutes of Health, Bethesda, MD, USA.
32
INSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
33
The Jackson Laboratory, Bar Harbor, ME, USA.
34
Sanford Imagenetics, Sanford Health, Sioux Falls, SD, USA.
35
Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.
36
Department of Genetics, University Medical Center Utrecht, the Netherlands.
37
Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.
38
Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
39
Mount Sinai School of Medicine, New York, NY, USA.
40
Institute of Cardiovascular Science, University College London, UK.
41
Child Neurology Unit. Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.
42
Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany.
43
Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.
44
Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada.
45
Centre for Rare Eye Diseases CARGO, SENSGENE FSMR Network, Strasbourg University Hospital, Strasbourg, France.
46
Immunology Service, Department of Laboratory Medicine, NIH Clinical Center, Bethesda, MD, USA.
47
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.
48
Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.

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.

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