The Human Phenotype Ontology in 2024: phenotypes around the world-Reference-Cited by-同舟云学术

The Human Phenotype Ontology in 2024: phenotypes around the world

Published:2023-11-11 Issue:D1 Volume:52 Page:D1333-D1346
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Gargano Michael A¹^ORCID,Matentzoglu Nicolas²^ORCID,Coleman Ben¹^ORCID,Addo-Lartey Eunice B³,Anagnostopoulos Anna V⁴^ORCID,Anderton Joel⁵^ORCID,Avillach Paul⁶^ORCID,Bagley Anita M⁷^ORCID,Bakštein Eduard⁸^ORCID,Balhoff James P⁹^ORCID,Baynam Gareth¹⁰,Bello Susan M⁴^ORCID,Berk Michael¹¹^ORCID,Bertram Holli¹²^ORCID,Bishop Somer¹³^ORCID,Blau Hannah¹^ORCID,Bodenstein David F¹⁴^ORCID,Botas Pablo¹⁵^ORCID,Boztug Kaan¹⁶^ORCID,Čady Jolana¹⁷^ORCID,Callahan Tiffany J¹⁸^ORCID,Cameron Rhiannon¹⁹^ORCID,Carbon Seth J²⁰^ORCID,Castellanos Francisco¹^ORCID,Caufield J Harry²⁰^ORCID,Chan Lauren E²¹^ORCID,Chute Christopher G²²^ORCID,Cruz-Rojo Jaime²³^ORCID,Dahan-Oliel Noémi²⁴^ORCID,Davids Jon R⁷^ORCID,de Dieuleveult Maud²⁵^ORCID,de Souza Vinicius²⁶,de Vries Bert B A²⁷^ORCID,de Vries Esther²⁸^ORCID,DePaulo J Raymond²⁹^ORCID,Derfalvi Beata³⁰^ORCID,Dhombres Ferdinand³¹^ORCID,Diaz-Byrd Claudia¹²^ORCID,Dingemans Alexander J M²⁷^ORCID,Donadille Bruno³²^ORCID,Duyzend Michael³³^ORCID,Elfeky Reem³⁴^ORCID,Essaid Shahim³⁵^ORCID,Fabrizzi Carolina³⁶^ORCID,Fico Giovanna³⁷^ORCID,Firth Helen V³⁸^ORCID,Freudenberg-Hua Yun³⁹^ORCID,Fullerton Janice M⁴⁰^ORCID,Gabriel Davera L⁴¹,Gilmour Kimberly⁴²^ORCID,Giordano Jessica⁴³^ORCID,Goes Fernando S²⁹^ORCID,Moses Rachel Gore⁴⁴^ORCID,Green Ian⁴⁵,Griese Matthias⁴⁶^ORCID,Groza Tudor¹⁰^ORCID,Gu Weihong⁴⁷,Guthrie Julia⁴⁸^ORCID,Gyori Benjamin⁴⁹^ORCID,Hamosh Ada⁵⁰^ORCID,Hanauer Marc³⁶^ORCID,Hanušová Kateřina¹⁷^ORCID,He Yongqun (Oliver)⁵¹^ORCID,Hegde Harshad²⁰^ORCID,Helbig Ingo⁵²^ORCID,Holasová Kateřina¹⁷^ORCID,Hoyt Charles Tapley⁴⁹^ORCID,Huang Shangzhi⁴⁷,Hurwitz Eric⁵³^ORCID,Jacobsen Julius O B⁵⁴^ORCID,Jiang Xiaofeng⁴⁷,Joseph Lisa⁵⁵^ORCID,Keramatian Kamyar⁵⁶^ORCID,King Bryan¹³^ORCID,Knoflach Katrin⁴⁶^ORCID,Koolen David A²⁷^ORCID,Kraus Megan L⁵³^ORCID,Kroll Carlo⁵⁴,Kusters Maaike⁴²^ORCID,Ladewig Markus S⁵⁷^ORCID,Lagorce David³⁶^ORCID,Lai Meng-Chuan⁵⁸^ORCID,Lapunzina Pablo⁵⁹^ORCID,Laraway Bryan⁵³^ORCID,Lewis-Smith David⁶⁰^ORCID,Li Xiarong⁴⁷,Lucano Caterina³⁶^ORCID,Majd Marzieh⁶¹^ORCID,Marazita Mary L⁵^ORCID,Martinez-Glez Victor⁶²^ORCID,McHenry Toby H⁵,McInnis Melvin G¹²^ORCID,McMurry Julie A⁵³^ORCID,Mihulová Michaela⁶³^ORCID,Millett Caitlin E⁶⁴^ORCID,Mitchell Philip B⁶⁵^ORCID,Moslerová Veronika⁶³^ORCID,Narutomi Kenji⁶⁶,Nematollahi Shahrzad⁶⁷^ORCID,Nevado Julian⁵⁹^ORCID,Nierenberg Andrew A⁶⁸^ORCID,Čajbiková Nikola Novák⁶³^ORCID,Nurnberger John I⁶⁹^ORCID,Ogishima Soichi⁷⁰^ORCID,Olson Daniel⁷¹^ORCID,Ortiz Abigail⁷²^ORCID,Pachajoa Harry⁷³^ORCID,Perez de Nanclares Guiomar⁷⁴^ORCID,Peters Amy⁷⁵^ORCID,Putman Tim⁵³^ORCID,Rapp Christina K⁴⁶,Rath Ana³⁶^ORCID,Reese Justin²⁰^ORCID,Rekerle Lauren¹^ORCID,Roberts Angharad M⁷⁶,Roy Suzy⁴⁵,Sanders Stephan J⁷⁷^ORCID,Schuetz Catharina⁷⁸^ORCID,Schulte Eva C⁷⁹^ORCID,Schulze Thomas G⁸⁰^ORCID,Schwarz Martin⁶³^ORCID,Scott Katie⁸¹^ORCID,Seelow Dominik⁸²^ORCID,Seitz Berthold⁸³^ORCID,Shen Yiping⁴⁷,Similuk Morgan N⁴⁴^ORCID,Simon Eric S⁸⁴^ORCID,Singh Balwinder⁸⁵^ORCID,Smedley Damian⁵⁴^ORCID,Smith Cynthia L⁴^ORCID,Smolinsky Jake T⁸⁶^ORCID,Sperry Sarah¹²^ORCID,Stafford Elizabeth⁸⁷^ORCID,Stefancsik Ray²⁶^ORCID,Steinhaus Robin⁸²^ORCID,Strawbridge Rebecca⁸⁸^ORCID,Sundaramurthi Jagadish Chandrabose¹^ORCID,Talapova Polina⁸⁹^ORCID,Tenorio Castano Jair A⁵⁹^ORCID,Tesner Pavel⁶³^ORCID,Thomas Rhys H⁶⁰^ORCID,Thurm Audrey⁵⁵^ORCID,Turnovec Marek⁶³^ORCID,van Gijn Marielle E⁹⁰^ORCID,Vasilevsky Nicole A⁹¹^ORCID,Vlčková Markéta⁶³^ORCID,Walden Anita³⁵^ORCID,Wang Kai⁴⁷^ORCID,Wapner Ron⁴³^ORCID,Ware James S⁷⁶^ORCID,Wiafe Addo A³,Wiafe Samuel A³^ORCID,Wiggins Lisa D⁹²^ORCID,Williams Andrew E⁸⁹^ORCID,Wu Chen⁴⁷,Wyrwoll Margot J⁹³^ORCID,Xiong Hui⁴⁷,Yalin Nefize⁸⁸^ORCID,Yamamoto Yasunori⁹⁴^ORCID,Yatham Lakshmi N⁵⁶^ORCID,Yocum Anastasia K¹²^ORCID,Young Allan H⁹⁵^ORCID,Yüksel Zafer⁹⁶^ORCID,Zandi Peter P²⁹^ORCID,Zankl Andreas⁹⁷^ORCID,Zarante Ignacio⁹⁸^ORCID,Zvolský Miroslav¹⁷^ORCID,Toro Sabrina⁵³^ORCID,Carmody Leigh C¹^ORCID,Harris Nomi L²⁰^ORCID,Munoz-Torres Monica C³⁵^ORCID,Danis Daniel¹^ORCID,Mungall Christopher J²⁰^ORCID,Köhler Sebastian⁹⁹^ORCID,Haendel Melissa A⁵³^ORCID,Robinson Peter N¹^ORCID

Affiliation:

1. The Jackson Laboratory for Genomic Medicine , Farmington , CT , USA

2. Semanticly , Athens , Greece

3. Rare Disease Ghana Initiative , Accra , Ghana

4. The Jackson Laboratory , Bar Harbor , ME , USA

5. Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh , Pittsburgh , PA , USA

6. Harvard Medical School , Boston, MA , USA

7. Shriners Children's Northern California , Sacramento , CA , USA

8. National Institute of Mental Health , Klecany , Czech Republic

9. Renaissance Computing Institute, University of North Carolina , Chapel Hill , NC 27517 , USA

10. Rare Care Centre, Perth Children's Hospital , Perth , Australia

11. Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine , Barwon Health, Geelong, Australia

12. Department of Psychiatry, University of Michigan , Ann Arbor , MI , USA

13. Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience , San Francisco , CA , USA

14. Department of Pharmacology and Toxicology, University of Toronto , Toronto , ON , Canada

15. Nostos Genomics GmbH , Berlin , Germany

16. St. Anna Children's Cancer Research Institute (CCRI) , Vienna , Austria

17. Institute of Health Information and Statistics of the Czech Republic , Prague , Czech Republic

18. Department of Biomedical Informatics, Columbia University Irving Medical Center , NY , NY , USA

19. Simon Fraser University , Burnaby , BC , Canada

20. Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA

21. College of Public Health and Human Sciences, Oregon State University , Corvallis , OR 97331 , USA

22. Schools of Medicine, Public Health, and Nursing, Johns Hopkins University , Baltimore , MD 21287 , USA

23. UDISGEN (Dysmorphology and Genetics Unit), 12 de Octubre Hospital , Madrid , Spain

24. Department of Clinical Research, Shriners Hospitals for Children , Montreal , Quebec , Canada

25. Département I&D, AP-HP, Banque Nationale de Données Maladies Rares , Paris , France

26. European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton CB10 1SD , UK

27. Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center , Nijmegen , Netherlands

28. Tranzo, TSB, Tilburg University , Netherlands

29. Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine , Baltimore , MD 21287 , USA

30. Department of Pediatrics, Dalhousie University , Halifax , NS , Canada

31. Fetal Medicine Department, Armand Trousseau Hospital , Sorbonne University, GRC26, INSERM, Limics, Paris , France

32. St Antoine Hospital, Reference Center for Rare Growth Endocrine Disorders, Sorbonne University, AP-HP, INSERM, US14 - Orphanet, Plateforme Maladies Rares , Paris , France

33. Massachusetts General Hospital , Boston , MA , USA

34. Department of Immunology, GOS Hospital for Children NHS Foundation Trust, University College London , London , UK

35. Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus , Aurora , CO 80045 , USA

36. INSERM, US14 - Orphanet, Plateforme Maladies Rares , Paris , France

37. Bipolar and Depressive Disorders Unit, Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM , Barcelona , Catalonia , Spain

38. Addenbrooke's Hospital, Cambridge University Hospitals , Cambridge , UK

39. Department of Psychiatry, Feinstein Institutes for Medical Research, Northwell Health, Manhasset , NY , USA

40. Neuroscience Research Australia , Sydney , NSW , Australia

41. School of Medicine, Johns Hopkins University , Baltimore , MD 21287 , USA

42. Immunology, NIHR Great Ormond Street Hospital BRC , London , UK

43. Department of Obstetrics and Gynecology, Columbia University Irving Medical Center , New York , NY , USA

44. National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda , MD 20892 , USA

45. SNOMED International , London W2 6BD , UK

46. Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL) , Munich , Germany

47. Chinese HPO Consortium , Beijing , China

48. Department of Structural and Computational Biology, University of Vienna; Max Perutz Labs , Vienna , Austria

49. Khoury College of Computer Sciences, Northeastern University , Boston , MA , USA

50. Department of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore , MD 21287 , USA

51. University of Michigan Medical School , Ann Arbor , MI , USA

52. Neurology, Children's Hospital of Philadelphia , Philadelphia , PA 19104 , USA

53. University of Colorado Anschutz Medical Campus , Aurora , CO 80045 , USA

54. William Harvey Research Institute, Queen Mary University of London , London , UK

55. Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD , USA

56. Department of Psychiatry, University of British Columbia , Vancouver , BC , Canada

57. Department of Ophthalmology, University Clinic Marburg - Campus Fulda , Fulda , Germany

58. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health , Toronto , ON , Canada

59. Institute of Medical and Molecular Genetics, Hospital Univ. La Paz , Madrid , Spain

60. Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University , Newcastle-Upon-Tyne NE14LP , UK

61. Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School , Boston , MA , USA

62. Center for Genomic Medicine, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA) , Sabadell , Spain

63. Department of Biology and Medical Genetics, 2nd Medical Faculty of Charles University and University Hospital Motol , Prague , Czech Republic

64. Feinstein Institutes for Medical Research, Northwell Health , Manhasset , NY , USA

65. Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine & Health, University of New South Wales , Sydney , NSW , Australia

66. Okinawa Prefectural Nanbu Medical Center & Children's Medical Center

67. School of Physical and Occupational Therapy, McGill University , Montreal , Quebec , Canada

68. Dauten Family Center for Bipolar Treatment Innovation, Massachusetts General Hospital , Boston , MA , USA

69. Stark Neurosciences Research Institute, Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis , IN , USA

70. INGEM/ToMMo, Tohoku University , Sendai , Japan

71. Data Collaboration Center, Data Science, Critical Path Institute , Tucson , AZ , USA

72. Department of Psychiatry, University of Toronto , Toronto , ON , Canada

73. Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad Icesi , Cali , Colombia

74. Molecular (epi) genetics lab, Bioaraba Health Research Institute, Araba University Hospital , Vitoria-Gasteiz, Spain

75. Department of Psychiatry, Massachusetts General Hospital , Boston , MA , USA

76. National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London , London W12 0HS , UK

77. Department of Paediatrics, Institute of Developmental and Regenerative Medicine, University of Oxford , Oxford , UK

78. Universitätsklinikum Carl Gustav Carus, Medizinische Fakultät, TU , Dresden , Germany

79. Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich , Munich , Germany

80. Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University , Syracuse , NY , USA

81. Department of Psychiatry, Dalhousie University , Halifax , NS , Canada

82. Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité , Berlin , Germany

83. Department of Ophthalmology, Saarland University Medical Center UKS , Homburg/Saar , Germany

84. Eisenberg Family Depression Center, University of Michigan , Ann Arbor , MI , USA

85. Department of Psychiatry and Psychology, Mayo Clinic , Rochester , MN , USA

86. Human Genetics Institute of New Jersey, Rutgers University , Piscataway , NJ , USA

87. The National Alliance on Mental Illness , Arlington , VA , USA

88. Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London , London , UK

89. Institute for Research and Health Policy Studies, Tufts Medicine , Boston , MA 2111 , USA

90. Department of Genetics, University Medical Center Groningen , Groningen , Netherlands

91. Critical Path Institute , Tucson , AZ , USA

92. National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention , Atlanta, GA, USA

93. Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh , Edinburgh , UK

94. Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems , Japan

95. Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London & South London and Maudsley NHS Foundation Trust, Bethlem Royal Hospital , Monks Orchard Road , Beckenham , Kent , London SE5 8AF , UK

96. Department of Human Genetics, Bioscientia Healthcare GmbH , Ingelheim , Germany

97. Faculty of Medicine and Health, The University of Sydney , Camperdown , Australia

98. Institute of Human Genetics, Pontificia Universidad Javeriana , Bogotá , Colombia

99. Ada Health GmbH , Berlin , Germany

Abstract

Abstract The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

Funder

NIH

French Ministry of Health

NHGRI

NCATS

Horizon 2020

Defense Advanced Research Projects Agency

DARPA Automating Scientific Knowledge Extraction and Modeling program

Berlin Institute of Health

Wellcome Trust

Angela Wright Bennett Foundation

McCusker Charitable Foundation