The Human Phenotype Ontology in 2024: phenotypes around the world

Michael A Gargano¹, Nicolas Matentzoglu², Ben Coleman¹, Eunice B Addo-Lartey³, Anna V Anagnostopoulos⁴, Joel Anderton⁵, Paul Avillach⁶, Anita M Bagley⁷, Eduard Bakštein⁸, James P Balhoff⁹, Gareth Baynam¹⁰, Susan M Bello⁴, Michael Berk¹¹, Holli Bertram¹², Somer Bishop¹³, Hannah Blau¹, David F Bodenstein¹⁴, Pablo Botas¹⁵, Kaan Boztug¹⁶, Jolana Čady¹⁷, Tiffany J Callahan¹⁸, Rhiannon Cameron¹⁹, Seth J Carbon²⁰, Francisco Castellanos¹, J Harry Caufield²⁰, Lauren E Chan²¹, Christopher G Chute²², Jaime Cruz-Rojo²³, Noémi Dahan-Oliel²⁴, Jon R Davids⁷, Maud de Dieuleveult²⁵, Vinicius de Souza²⁶, Bert B A de Vries²⁷, Esther de Vries²⁸, J Raymond DePaulo²⁹, Beata Derfalvi³⁰, Ferdinand Dhombres³¹, Claudia Diaz-Byrd¹², Alexander J M Dingemans²⁷, Bruno Donadille³², Michael Duyzend³³, Reem Elfeky³⁴, Shahim Essaid³⁵, Carolina Fabrizzi³⁶, Giovanna Fico³⁷, Helen V Firth³⁸, Yun Freudenberg-Hua³⁹, Janice M Fullerton⁴⁰, Davera L Gabriel⁴¹, Kimberly Gilmour⁴², Jessica Giordano⁴³, Fernando S Goes²⁹, Rachel Gore Moses⁴⁴, Ian Green⁴⁵, Matthias Griese⁴⁶, Tudor Groza¹⁰, Weihong Gu⁴⁷, Julia Guthrie⁴⁸, Benjamin Gyori⁴⁹, Ada Hamosh⁵⁰, Marc Hanauer³⁶, Kateřina Hanušová¹⁷, Yongqun Oliver He⁵¹, Harshad Hegde²⁰, Ingo Helbig⁵², Kateřina Holasová¹⁷, Charles Tapley Hoyt⁴⁹, Shangzhi Huang⁴⁷, Eric Hurwitz⁵³, Julius O B Jacobsen⁵⁴, Xiaofeng Jiang⁴⁷, Lisa Joseph⁵⁵, Kamyar Keramatian⁵⁶, Bryan King¹³, Katrin Knoflach⁴⁶, David A Koolen²⁷, Megan L Kraus⁵³, Carlo Kroll⁵⁴, Maaike Kusters⁴², Markus S Ladewig⁵⁷, David Lagorce³⁶, Meng-Chuan Lai⁵⁸, Pablo Lapunzina⁵⁹, Bryan Laraway⁵³, David Lewis-Smith⁶⁰, Xiarong Li⁴⁷, Caterina Lucano³⁶, Marzieh Majd⁶¹, Mary L Marazita⁵, Victor Martinez-Glez⁶², Toby H McHenry⁵, Melvin G McInnis¹², Julie A McMurry⁵³, Michaela Mihulová⁶³, Caitlin E Millett⁶⁴, Philip B Mitchell⁶⁵, Veronika Moslerová⁶³, Kenji Narutomi⁶⁶, Shahrzad Nematollahi⁶⁷, Julian Nevado⁵⁹, Andrew A Nierenberg⁶⁸, Nikola Novák Čajbiková⁶³, John I Nurnberger Jr⁶⁹, Soichi Ogishima⁷⁰, Daniel Olson⁷¹, Abigail Ortiz⁷², Harry Pachajoa⁷³, Guiomar Perez de Nanclares⁷⁴, Amy Peters⁷⁵, Tim Putman⁵³, Christina K Rapp⁴⁶, Ana Rath³⁶, Justin Reese²⁰, Lauren Rekerle¹, Angharad M Roberts⁷⁶, Suzy Roy⁴⁵, Stephan J Sanders⁷⁷, Catharina Schuetz⁷⁸, Eva C Schulte⁷⁹, Thomas G Schulze⁸⁰, Martin Schwarz⁶³, Katie Scott⁸¹, Dominik Seelow⁸², Berthold Seitz⁸³, Yiping Shen⁴⁷, Morgan N Similuk⁴⁴, Eric S Simon⁸⁴, Balwinder Singh⁸⁵, Damian Smedley⁵⁴, Cynthia L Smith⁴, Jake T Smolinsky⁸⁶, Sarah Sperry¹², Elizabeth Stafford⁸⁷, Ray Stefancsik²⁶, Robin Steinhaus⁸², Rebecca Strawbridge⁸⁸, Jagadish Chandrabose Sundaramurthi¹, Polina Talapova⁸⁹, Jair A Tenorio Castano⁵⁹, Pavel Tesner⁶³, Rhys H Thomas⁶⁰, Audrey Thurm⁵⁵, Marek Turnovec⁶³, Marielle E van Gijn⁹⁰, Nicole A Vasilevsky⁹¹, Markéta Vlčková⁶³, Anita Walden³⁵, Kai Wang⁴⁷, Ron Wapner⁴³, James S Ware⁷⁶, Addo A Wiafe³, Samuel A Wiafe³, Lisa D Wiggins⁹², Andrew E Williams⁸⁹, Chen Wu⁴⁷, Margot J Wyrwoll⁹³, Hui Xiong⁴⁷, Nefize Yalin⁸⁸, Yasunori Yamamoto⁹⁴, Lakshmi N Yatham⁵⁶, Anastasia K Yocum¹², Allan H Young⁹⁵, Zafer Yüksel⁹⁶, Peter P Zandi²⁹, Andreas Zankl⁹⁷, Ignacio Zarante⁹⁸, Miroslav Zvolský¹⁷, Sabrina Toro⁵³, Leigh C Carmody¹, Nomi L Harris²⁰, Monica C Munoz-Torres³⁵, Daniel Danis¹, Christopher J Mungall²⁰, Sebastian Köhler⁹⁹, Melissa A Haendel⁵³, Peter N Robinson¹

Affiliations

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.

PMID: 37953324
PMCID: PMC10767975
DOI: 10.1093/nar/gkad1005

The Human Phenotype Ontology in 2024: phenotypes around the world

Michael A Gargano et al. Nucleic Acids Res. 2024.

. 2024 Jan 5;52(D1):D1333-D1346.

doi: 10.1093/nar/gkad1005.

Authors

Affiliations

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.

PMID: 37953324
PMCID: PMC10767975
DOI: 10.1093/nar/gkad1005

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.

PubMed Disclaimer

Figures

**Figure 1.**
Screenshot of internationalized HPO Web application. For each term, users can choose from the available languages (seven, in this example) in addition to English. Term labels, definitions and synonyms are shown in the chosen language if translations are available; otherwise, the English version is shown.

**Figure 2.**
The Phenotypic Feature element of the GA4GH Phenopacket Schema. This element contextualizes HPO annotations by allowing the severity, onset, resolution, and other characteristics (modifiers) of the phenotypic observation to be specified. In this example, two phenotypic observations are given: (i) severe, daily (quotidian) infantile spasms with infantile onset (between month two and twelve of life) and resolution at the age of 4 years, 2 months and (ii) exclusion of global developmental delay (that is, this feature was assessed and explicitly found not to be present).

See this image and copyright information in PMC

References

1. Shefchek K.A., Harris N.L., Gargano M., Matentzoglu N., Unni D., Brush M., Keith D., Conlin T., Vasilevsky N., Zhang X.A.et al.. The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2020; 48:D704–D715. - PMC - PubMed
1. Philippakis A.A., Azzariti D.R., Beltran S., Brookes A.J., Brownstein C.A., Brudno M., Brunner H.G., Buske O.J., Carey K., Doll C.et al.. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum. Mutat. 2015; 36:915–921. - PMC - PubMed
1. Robinson P.N., Köhler S., Bauer S., Seelow D., Horn D., Mundlos S.. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am. J. Hum. Genet. 2008; 83:610–615. - PMC - PubMed
1. Köhler S., Carmody L., Vasilevsky N., Jacobsen J.O.B., Danis D., Gourdine J.-P., Gargano M., Harris N.L., Matentzoglu N., McMurry J.A.et al.. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2019; 47:D1018–D1027. - PMC - PubMed
1. Köhler S., Gargano M., Matentzoglu N., Carmody L.C., Lewis-Smith D., Vasilevsky N.A., Danis D., Balagura G., Baynam G., Brower A.M.et al.. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021; 49:D1207–D1217. - PMC - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions

Grants and funding

LinkOut - more resources

Full Text Sources

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

The Human Phenotype Ontology in 2024: phenotypes around the world

Affiliations

The Human Phenotype Ontology in 2024: phenotypes around the world

Authors

Affiliations

Abstract

Figures

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources