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PMID: 24217912 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Nucleic acids research ·Vol. 42 ·No. Database issue ·2014-01-00 ·Pages D966-74

Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN

Abstract

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.

MeSH Terms
Animals Biological Ontologies Databases, Factual Genetic Diseases, Inborn/diagnosis,genetics Genomics Humans Internet Mice Phenotype
Authors & Affiliations
47 authors, click to expand affiliations / ORCID
Köhler Sebastian
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
Doelken Sandra C
Mungall Christopher J
Bauer Sebastian
Firth Helen V
Bailleul-Forestier Isabelle
Black Graeme C M
Brown Danielle L
Brudno Michael
Campbell Jennifer
FitzPatrick David R
Eppig Janan T
Jackson Andrew P
Freson Kathleen
Girdea Marta
Helbig Ingo
Hurst Jane A
Jähn Johanna
Jackson Laird G
Kelly Anne M
Ledbetter David H
Mansour Sahar
Martin Christa L
Moss Celia
Mumford Andrew
Ouwehand Willem H
Park Soo-Mi
Riggs Erin Rooney
Scott Richard H
Sisodiya Sanjay
Van Vooren Steven
Wapner Ronald J
Wilkie Andrew O M
Wright Caroline F
Vulto-van Silfhout Anneke T
de Leeuw Nicole
de Vries Bert B A
Washingthon Nicole L
Smith Cynthia L
Westerfield Monte
Schofield Paul
Ruef Barbara J
Gkoutos Georgios V
Haendel Melissa
Smedley Damian
Lewis Suzanna E
Robinson Peter N
References (33)
33 references, click to expand
  1. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.
    Am J Hum Genet. 2008 Nov;83(5):610-5 PMID: 18950739
  2. PhenoTips: patient phenotyping software for clinical and research use.
    Hum Mutat. 2013 Aug;34(8):1057-65 PMID: 23636887
  3. McKusick's Online Mendelian Inheritance in Man (OMIM).
    Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6 PMID: 18842627
  4. Characterization of the proteome, diseases and evolution of the human postsynaptic density.
    Nat Neurosci. 2011 Jan;14(1):19-21 PMID: 21170055
  5. Towards a Universal Clinical Genomics Database: the 2012 International Standards for Cytogenomic Arrays Consortium Meeting.
    Hum Mutat. 2013 Jun;34(6):915-9 PMID: 23463607
  6. Type II sialidosis: review of the clinical spectrum and identification of a new splicing defect with chitotriosidase assessment in two patients.
    J Neurol. 2009 Nov;256(11):1911-5 PMID: 19568825
  7. PhenomeNET: a whole-phenome approach to disease gene discovery.
    Nucleic Acids Res. 2011 Oct;39(18):e119 PMID: 21737429
  8. Representation of rare diseases in health information systems: the Orphanet approach to serve a wide range of end users.
    Hum Mutat. 2012 May;33(5):803-8 PMID: 22422702
  9. Entity/quality-based logical definitions for the human skeletal phenome using PATO.
    Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:7069-72 PMID: 19964203
  10. Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish.
    Dis Model Mech. 2013 Mar;6(2):358-72 PMID: 23104991
  11. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources.
    Am J Hum Genet. 2009 Apr;84(4):524-33 PMID: 19344873
  12. PREDICT: a method for inferring novel drug indications with application to personalized medicine.
    Mol Syst Biol. 2011 Jun 07;7:496 PMID: 21654673
  13. Clinical diagnostics in human genetics with semantic similarity searches in ontologies.
    Am J Hum Genet. 2009 Oct;85(4):457-64 PMID: 19800049
  14. DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more.
    Nucleic Acids Res. 2013 Jan;41(Database issue):D536-44 PMID: 23161684
  15. Ontological phenotype standards for neurogenetics.
    Hum Mutat. 2012 Sep;33(9):1333-9 PMID: 22573485
  16. The Gene Ontology (GO) database and informatics resource.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61 PMID: 14681407
  17. Linking human diseases to animal models using ontology-based phenotype annotation.
    PLoS Biol. 2009 Nov;7(11):e1000247 PMID: 19956802
  18. Disease Ontology: a backbone for disease semantic integration.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D940-6 PMID: 22080554
  19. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
    Nat Biotechnol. 2007 Nov;25(11):1251-5 PMID: 17989687
  20. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®).
    Hum Mutat. 2011 May;32(5):564-7 PMID: 21472891
  21. Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience.
    Hum Mutat. 2012 May;33(5):787-96 PMID: 22331816
  22. MouseFinder: Candidate disease genes from mouse phenotype data.
    Hum Mutat. 2012 May;33(5):858-66 PMID: 22331800
  23. A reference ontology for biomedical informatics: the Foundational Model of Anatomy.
    J Biomed Inform. 2003 Dec;36(6):478-500 PMID: 14759820
  24. Bayesian ontology querying for accurate and noise-tolerant semantic searches.
    Bioinformatics. 2012 Oct 1;28(19):2502-8 PMID: 22843981
  25. Deep phenotyping for precision medicine.
    Hum Mutat. 2012 May;33(5):777-80 PMID: 22504886
  26. PhenoDigm: analyzing curated annotations to associate animal models with human diseases.
    Database (Oxford). 2013 May 09;2013:bat025 PMID: 23660285
  27. A knowledge based approach to matching human neurodegenerative disease and animal models.
    Front Neuroinform. 2013 May 14;7:7 PMID: 23717278
  28. Improving ontologies by automatic reasoning and evaluation of logical definitions.
    BMC Bioinformatics. 2011 Oct 27;12:418 PMID: 22032770
  29. The Deciphering Developmental Disorders (DDD) study.
    Dev Med Child Neurol. 2011 Aug;53(8):702-3 PMID: 21679367
  30. Strategies for exome and genome sequence data analysis in disease-gene discovery projects.
    Clin Genet. 2011 Aug;80(2):127-32 PMID: 21615730
  31. Phenotype matters.
    Nat Genet. 2004 Apr;36(4):323-4 PMID: 15054484
  32. An update on ECARUCA, the European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations.
    Eur J Med Genet. 2013 Sep;56(9):471-4 PMID: 23851227
  33. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.
    F1000Res. 2013 Feb 01;2:30 PMID: 24358873
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
Published
2014-01-00
Epub
2013-00-11
Pages
D966-74
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3965098
Subset
IM
Grants
Department of Health · RP-PG-0310-1002 · United Kingdom
NIH HHS · R24-OD011883 · United States
NHGRI NIH HHS · R01-HG004838 · United States
NHGRI NIH HHS · U41 HG000330 · United States
NIH HHS · R24 OD011883 · United States
NHGRI NIH HHS · U41 HG002659 · United States
British Heart Foundation · RG/09/012/28096 · United Kingdom
Medical Research Council · MC_PC_U127580972 · United Kingdom
NHGRI NIH HHS · HG000330 · United States
NIMH NIH HHS · R01 MH074090 · United States
NHGRI NIH HHS · P41 HG002659 · United States
NHGRI NIH HHS · U41-HG002659 · United States
Medical Research Council · MC_PC_U127561093 · United Kingdom
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