The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.
(PMID:26119816 PMCID:PMC4572507)
PMID:26119816 PMCID:PMC4572507
Tudor Groza
School of Information Technology and Electrical Engineering, University of Queensland, St. Lucia, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.
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Sebastian Köhler
Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
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Dawid Moldenhauer
Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; University of Applied Sciences, Wiesenstrasse 14, 35390 Giessen, Germany.
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Nicole Vasilevsky
National University of Natural Medicine
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Gareth Baynam
School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6840, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Office of Population Health Genomics, Public Health and Clinical Services Division, Department of Health, Perth, WA 6004, Australia; Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; Telethon Kids Institute, Perth, WA 6008, Australia.
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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.
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Lynn Schriml
University of Maryland Baltimore
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Warren Alden Kibbe
Center for Biomedical Informatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA.
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Paul N Schofield
Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; The Jackson Laboratory, Bar Harbor, ME 04609, USA.
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Drashtti Vasant
European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
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Anthony J Brookes
Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.
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Andreas Zankl
Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Academic Department of Medical Genetics, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2145, Australia.
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Nicole L Washington
Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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Christopher J Mungall
Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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Suzanna E Lewis
Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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Melissa A Haendel
Library, Oregon Health & Science University, Portland, OR 97239, USA.
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Helen Parkinson
European Bioinformatics Institute
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Peter N Robinson
Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany. Electronic address: peter.robinson@charite.de.
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Affiliations
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1. School of Information Technology and Electrical Engineering, University of Queensland, St. Lucia, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.
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2. Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
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3. Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; University of Applied Sciences, Wiesenstrasse 14, 35390 Giessen, Germany.
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4. Library, Oregon Health & Science University, Portland, OR 97239, USA.
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5. School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6840, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Office of Population Health Genomics, Public Health and Clinical Services Division, Department of Health, Perth, WA 6004, Australia; Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; Telethon Kids Institute, Perth, WA 6008, Australia.
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6. 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.
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7. Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
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8. Center for Biomedical Informatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA.
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9. Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; The Jackson Laboratory, Bar Harbor, ME 04609, USA.
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10. Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.
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11. European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK.
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12. Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Academic Department of Medical Genetics, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2145, Australia.
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13. Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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14. Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany. Electronic address: peter.robinson@charite.de.
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American Journal of Human Genetics
[25 Jun 2015, 97(1):111-124]
2015/08
Type:
Research Support, Non-U.S. Gov't, research-article, Journal Article
DOI: 10.1016/j.ajhg.2015.05.020
DOI: 10.1016/j.ajhg.2015.05.020
Abstract
The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.
Funding
