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

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gkt1026· OSTI ID:1625512
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  1. Charite-Universitatsmedizin Berlin (Germany). Inst. for Medical Genetics and Human Genetics; Charite-Universitatsmedizin Berlin (Germany). Berlin-Brandenburg Center for Regeneratice Therapies; DOE/OSTI
  2. Charite-Universitatsmedizin Berlin (Germany). Inst. for Medical Genetics and Human Genetics
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. The Wellcome Trust Sanger Inst., Cambridgeshire (United States). Wellcome Trust Genome Campus; Cambridge Univ. (United Kingdom). Addenbrooke's Hospital. Dept. of Medical Genetics
  5. Universite Paul Sabatier, Toulouse (France). Faculte de Chirurgie Dentaire
  6. Manchester Academic Health Sciences Centre (MAHSC), Manchester (United Kingdom). Central Manchester Univ. Hospitals NHS Foundation Trust. Centre for Genomic Medicine; Univ. of Manchester (United Kingdom). Faculty of Medical and Human Scienes. Inst. of Human Development. Centre for Genomic Medicine
  7. Newcastle Univ. (United Kingdom). Inst. of Genetic Medicine
  8. Univ. of Toronto, ON (Canada). Dept. of Computer Science; Hospital for Sick Children, Toronto, ON (Canada). Centre for Computational Medicine
  9. Newcastle Univ. (United Kingdom). Inst. of Genetic Medicine; Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom). Dept. of Clinical Genetics
  10. Univ. of Edinburgh, Scotland (United Kingdom). MRC Inst. of Genetic and Molecular Medicine. MRC Human Genetics Unit
  11. The Jackson Lab., Bar Harbor, ME (United States)
  12. Univ. of Leuven (Belgium). Center for Molecular and Vascular Biology
  13. Univ. Medical Center Schleswig-Holstein, Kiel (Germany). Dept.of Neuropediatrics
  14. Great Ormond Street Hospital, London (United Kingdom). NE Thames Genetics Service
  15. Drexel Univ., Philadelphia, PA (United States). College of Medicine
  16. Univ. of Cambridge (United Kingdom). NHS Blood and Transplant Cambridge. Dept. of Haematology
  17. Geisinger Health System, Danville, PA (United States). Autism and Developmental Medicine Inst.
  18. St George’s Healthcare NHS Trust, Tooting, London (United Kingdom). SW Thames REgional Genetics Service
  19. Birmingham Children’s Hospital, Birmingham (United Kingdom). Dept. of Dermatology
  20. Bristol Univ. (United Kingdom). Bristol Heart Inst.
  21. The Wellcome Trust Sanger Inst., Cambridgeshire (United States). Wellcome Trust Genome Campus; Univ. of Cambridge (United Kingdom). NHS Blood and Transplant. Dept. of Haematology
  22. Univ. of Cambridge (United Kingdom). Dept. of Medical Genetics
  23. Univ. College London (United Kingdom). Inst. of Child Health. London Clinical and Molecular Genetics Unit. Great Ormond Street Hospital. Dept. of Clinical Genetics
  24. Univ. College London (United Kingdom). Inst. of Neurology. Dept. of Clincial and Experimental Epilepsy
  25. Cartagenia, Leuven (Belgium)
  26. Columbia Univ., New York, NY (United States). Medical Center. Dept. of Obstetrics and Gynecology
  27. Univ. of Oxford (United Kingdom). John Radcliffe Hospital. Weatherall Inst. of Molecular Medicine
  28. The Wellcome Trust Sanger Inst., Cambridgeshire (United States). Wellcome Trust Genome Campus
  29. Radboud Univ., Nijmegen (Netherlands). Medical Center. Dept. of Human Genetics
  30. The Jackson Laboratory, Bar Harbor, ME (United States)
  31. Univ. of Oregon, Eugene, OR (United States). ZFIN
  32. The Jackson Laboratory, Bar Harbor, ME (United States); Univ. of Cambridge (United Kingdom). Dept. of Physiology, Development and Neuroscience
  33. Aberystwyth Univ. (United Kingdom). Dept. of Computer Science
  34. Oregon Health & Science University, Portland, OR (United States). Dept. of Medical Informatics and Clinical Epidemiology
  35. Charite-Universitatsmedizin Berlin (Germany). Inst. for Medical Genetics and Human Genetics; Charite-Universitatsmedizin Berlin (Germany). Berlin-Brandenburg Center for Regeneratice Therapies; Max Planck Inst. for Molecular Genetics, Berlin (Germany)
+ Show Author Affiliations
The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and welldefined 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.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625512
Journal Information:
Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 42; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
The Human Phenotype Ontology (HPO) project