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

Sebastian Köhler¹, Sandra C Doelken, Christopher J Mungall, Sebastian Bauer, Helen V Firth, Isabelle Bailleul-Forestier, Graeme C M Black, Danielle L Brown, Michael Brudno, Jennifer Campbell, David R FitzPatrick, Janan T Eppig, Andrew P Jackson, Kathleen Freson, Marta Girdea, Ingo Helbig, Jane A Hurst, Johanna Jähn, Laird G Jackson, Anne M Kelly, David H Ledbetter, Sahar Mansour, Christa L Martin, Celia Moss, Andrew Mumford, Willem H Ouwehand, Soo-Mi Park, Erin Rooney Riggs, Richard H Scott, Sanjay Sisodiya, Steven Van Vooren, Ronald J Wapner, Andrew O M Wilkie, Caroline F Wright, Anneke T Vulto-van Silfhout, Nicole de Leeuw, Bert B A de Vries, Nicole L Washingthon, Cynthia L Smith, Monte Westerfield, Paul Schofield, Barbara J Ruef, Georgios V Gkoutos, Melissa Haendel, Damian Smedley, Suzanna E Lewis, Peter N Robinson

Affiliations

Affiliation

¹ 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

PMID: 24217912
PMCID: PMC3965098
DOI: 10.1093/nar/gkt1026

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

Sebastian Köhler et al. Nucleic Acids Res. 2014 Jan.

. 2014 Jan;42(Database issue):D966-74.

doi: 10.1093/nar/gkt1026. Epub 2013 Nov 11.

Authors

Affiliation

¹ 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

PMID: 24217912
PMCID: PMC3965098
DOI: 10.1093/nar/gkt1026

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.

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Figures

**Figure 1.**
The HPO aims to act as a central resource to connect several genomics datasets with the diseasome. Thus, the HPO can act as a scaffold for enabling the interoperability between molecular biology and human disease. For example, phenotypic abnormalities in genetically modified model organisms can be mapped to human disease phenotypes (2).

**Figure 2.**
Statistics of the data from the HPO project from January 2009 to August 2013. Ontology statistics shows quantities related to the file hp.obo. The annotation statistics clearly demonstrates the inclusion of Orphanet data in October 2012.

See this image and copyright information in PMC

References

1. Amberger J, Bocchini CA, Hamosh A. A new face and new challenges for online mendelian inheritance in man (OMIM®) Hum. Mutat. 2011;32:564–567. - PubMed
1. Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, et al. 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;6:358–372. - PMC - PubMed
1. Biesecker LG. Phenotype matters. Nat. Genet. 2004;36:323–324. - PubMed
1. Robinson PN. Deep phenotyping for precision medicine. Hum. Mutat. 2012;33:777–780. - PubMed
1. Gene Ontology Consortium. The gene ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32:D258–D261. - PMC - PubMed

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

Affiliation

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

Authors

Affiliation

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Molecular Biology Databases