The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.
The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online.
Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke's Hospital, Cambridge CB2 2QQ, UK, Université Paul Sabatier, Faculté de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine. Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada, Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds LS2 9NS, UK, MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Center for Molecular and Vascular Biology, University of Leuven, Belgium, Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel Campus, 24105 Kiel, Germany, NE Thames Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK, Drexel University College of Medicine, Philadelphia, PA 19102, USA, Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge, CB2 0PT Cambridge, UK, Autism and Developmental Medicine Institute, Geisinger Health System
Sebastian
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Köhler
Sandra C
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Doelken
Christopher J
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Mungall
Sebastian
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Bauer
Helen V
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Firth
Isabelle
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Bailleul-Forestier
Graeme C M
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Black
Danielle L
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Brown
Michael
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Brudno
Jennifer
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Campbell
David R
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FitzPatrick
Janan T
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Eppig
Andrew P
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Jackson
Kathleen
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Freson
Marta
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Girdea
Ingo
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Helbig
Jane A
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Hurst
Johanna
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Jähn
Laird G
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Jackson
Anne M
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Kelly
David H
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Ledbetter
Sahar
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Mansour
Christa L
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Martin
Celia
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Moss
Andrew
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Mumford
Willem H
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Ouwehand
Soo-Mi
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Park
Erin Rooney
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Riggs
Richard H
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Scott
Sanjay
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Sisodiya
Steven
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Van Vooren
Ronald J
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Wapner
Andrew O M
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Wilkie
Caroline F
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Wright
Anneke T
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Vulto-van Silfhout
Nicole
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de Leeuw
Bert B A
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de Vries
Nicole L
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Washingthon
Cynthia L
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Smith
Monte
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Westerfield
Paul
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Schofield
Barbara J
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Ruef
Georgios V
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Gkoutos
Melissa
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Haendel
Damian
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Smedley
Suzanna E
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Lewis
Peter N
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Robinson
D000818:Animals; D064229:Biological Ontologies; D016208:Databases, Factual; D030342:Genetic Diseases, Inborn / Q000175:diagnosis / Q000235:genetics*; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D010641:Phenotype