The Human Phenotype Ontology in 2024: phenotypes around the world.
Journal: Nucleic acids research
Volume: 52
Issue: D1
Year of Publication: 2024
Affiliated Institutions: The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. Semanticly, Athens, Greece. Rare Disease Ghana Initiative, Accra, Ghana. The Jackson Laboratory, Bar Harbor, ME, USA. Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA. Harvard Medical School, Boston, MA, USA. Shriners Children's Northern California, Sacramento, CA, USA. National Institute of Mental Health, Klecany, Czech Republic. Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC , USA. Rare Care Centre, Perth Children's Hospital, Perth, Australia. Deakin University, IMPACT - the Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Geelong, Australia. Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA. Department of Psychiatry and Behavioral Sciences, UCSF Weil Institute for Neuroscience, San Francisco, CA, USA. Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada. Nostos Genomics GmbH, Berlin, Germany. St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria. Institute of Health Information and Statistics of the Czech Republic, Prague, Czech Republic. Department of Biomedical Informatics, Columbia University Irving Medical Center, NY, NY, USA. Simon Fraser University, Burnaby, BC, Canada. Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA , USA. College of Public Health and Human Sciences, Oregon State University, Corvallis, OR , USA. Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD , USA. UDISGEN (Dysmorphology and Genetics Unit), de Octubre Hospital, Madrid, Spain. Department of Clinical Research, Shriners Hospitals for Children, Montreal, Quebec, Canada. Département I&D, AP-HP, Banque Nationale de Données Maladies Rares, Paris, France. European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB SD, UK. Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands. Tranzo, TSB, Tilburg University, Netherlands. Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD , USA. Department of Pediatrics, Dalhousie University, Halifax, NS, Canada. Fetal Medicine Department, Armand Trousseau Hospital, Sorbonne University, GRC, INSERM, Limics, Paris, France. St Antoine Hospital, Reference Center for Rare Growth Endocrine Disorders, Sorbonne University, AP-HP, INSERM, US - Orphanet, Plateforme Maladies Rares, Paris, France. Massachusetts General Hospital, Boston, MA, USA. Department of Immunology, GOS Hospital for Children NHS Foundation Trust, University College London, London, UK. Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO , USA. INSERM, US - Orphanet, Plateforme Maladies Rares, Paris, France. Bipolar and Depressive Disorders Unit, Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Catalonia, Spain. Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK. Department of Psychiatry, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA. Neuroscience Research Australia, Sydney, NSW, Australia. School of Medicine, Johns Hopkins University, Baltimore, MD , USA. Immunology, NIHR Great Ormond Street Hospital BRC, London, UK. Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA. National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD , USA. SNOMED International, London W BD, UK. Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, German center for Lung research (DZL), Munich, Germany. Chinese HPO Consortium, Beijing, China. Department of Structural and Computational Biology, University of Vienna; Max Perutz Labs, Vienna, Austria. Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA. Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD , USA. University of Michigan Medical School, Ann Arbor, MI, USA. Neurology, Children's Hospital of Philadelphia, Philadelphia, PA , USA. University of Colorado Anschutz Medical Campus, Aurora, CO , USA. William Harvey Research Institute, Queen Mary University of London, London, UK. Neurodevelopmental and Behavioral Phenotyping Service, National Institute of Mental Health, Bethesda, MD, USA. Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada. Department of Ophthalmology, University Clinic Marburg - Campus Fulda, Fulda, Germany. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada. Institute of Medical and Molecular Genetics, Hospital Univ. La Paz, Madrid, Spain. Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University, Newcastle-Upon-Tyne NELP, UK. Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Center for Genomic Medicine, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (IPT-CERCA), Sabadell, Spain. Department of Biology and Medical Genetics, nd Medical Faculty of Charles University and University Hospital Motol, Prague, Czech Republic. Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA. Discipline of Psychiatry & Mental Health, School of Clinical Medicine, Faculty of Medicine & Health, University of New South Wales, Sydney, NSW, Australia. Okinawa Prefectural Nanbu Medical Center & Children's Medical Center. School of Physical and Occupational Therapy, McGill University, Montreal, Quebec, Canada. Dauten Family Center for Bipolar Treatment Innovation, Massachusetts General Hospital, Boston, MA, USA. Stark Neurosciences Research Institute, Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA. INGEM/ToMMo, Tohoku University, Sendai, Japan. Data Collaboration Center, Data Science, Critical Path Institute, Tucson, AZ, USA. Department of Psychiatry, University of Toronto, Toronto, ON, Canada. Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Universidad Icesi, Cali, Colombia. Molecular (epi) genetics lab, Bioaraba Health Research Institute, Araba University Hospital, Vitoria-Gasteiz, Spain. Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA. National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London W HS, UK. Department of Paediatrics, Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK. Universitätsklinikum Carl Gustav Carus, Medizinische Fakultät, TU, Dresden, Germany. Institute of Psychiatric Phenomics and Genomics (IPPG), LMU University Hospital, LMU Munich, Munich, Germany. Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA. Department of Psychiatry, Dalhousie University, Halifax, NS, Canada. Exploratory Diagnostic Sciences, Berliner Institut für Gesundheitsforschung - Charité, Berlin, Germany. Department of Ophthalmology, Saarland University Medical Center UKS, Homburg/Saar, Germany. Eisenberg Family Depression Center, University of Michigan, Ann Arbor, MI, USA. Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA. Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA. The National Alliance on Mental Illness, Arlington, VA, USA. Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK. Institute for Research and Health Policy Studies, Tufts Medicine, Boston, MA , USA. Department of Genetics, University Medical Center Groningen, Groningen, Netherlands. Critical Path Institute, Tucson, AZ, USA. National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA. Centre for Regenerative Medicine, Institute for Regeneration and Repair, Institute for Stem Cell Research, University of Edinburgh, Edinburgh, UK. Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Japan. 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 SE AF, UK. Department of Human Genetics, Bioscientia Healthcare GmbH, Ingelheim, Germany. Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia. Institute of Human Genetics, Pontificia Universidad Javeriana, Bogotá, Colombia. Ada Health GmbH, Berlin, Germany.
Abstract summary
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.Authors & Co-authors: Gargano Michael A MA Matentzoglu Nicolas N Coleman Ben B Addo-Lartey Eunice B EB Anagnostopoulos Anna V AV Anderton Joel J Avillach Paul P Bagley Anita M AM Bakštein Eduard E Balhoff James P JP Baynam Gareth G Bello Susan M SM Berk Michael M Bertram Holli H Bishop Somer S Blau Hannah H Bodenstein David F DF Botas Pablo P Boztug Kaan K Čady Jolana J Callahan Tiffany J TJ Cameron Rhiannon R Carbon Seth J SJ Castellanos Francisco F Caufield J Harry JH Chan Lauren E LE Chute Christopher G CG Cruz-Rojo Jaime J Dahan-Oliel Noémi N Davids Jon R JR de Dieuleveult Maud M de Souza Vinicius V de Vries Bert B A BBA de Vries Esther E DePaulo J Raymond JR Derfalvi Beata B Dhombres Ferdinand F Diaz-Byrd Claudia C Dingemans Alexander J M AJM Donadille Bruno B Duyzend Michael M Elfeky Reem R Essaid Shahim S Fabrizzi Carolina C Fico Giovanna G Firth Helen V HV Freudenberg-Hua Yun Y Fullerton Janice M JM Gabriel Davera L DL Gilmour Kimberly K Giordano Jessica J Goes Fernando S FS Moses Rachel Gore RG Green Ian I Griese Matthias M Groza Tudor T Gu Weihong W Guthrie Julia J Gyori Benjamin B Hamosh Ada A Hanauer Marc M Hanušová Kateřina K He Yongqun Oliver YO Hegde Harshad H Helbig Ingo I Holasová Kateřina K Hoyt Charles Tapley CT Huang Shangzhi S Hurwitz Eric E Jacobsen Julius O B JOB Jiang Xiaofeng X Joseph Lisa L Keramatian Kamyar K King Bryan B Knoflach Katrin K Koolen David A DA Kraus Megan L ML Kroll Carlo C Kusters Maaike M Ladewig Markus S MS Lagorce David D Lai Meng-Chuan MC Lapunzina Pablo P Laraway Bryan B Lewis-Smith David D Li Xiarong X Lucano Caterina C Majd Marzieh M Marazita Mary L ML Martinez-Glez Victor V McHenry Toby H TH McInnis Melvin G MG McMurry Julie A JA Mihulová Michaela M Millett Caitlin E CE Mitchell Philip B PB Moslerová Veronika V Narutomi Kenji K Nematollahi Shahrzad S Nevado Julian J Nierenberg Andrew A AA Čajbiková Nikola Novák NN Nurnberger John I JI Ogishima Soichi S Olson Daniel D Ortiz Abigail A Pachajoa Harry H Perez de Nanclares Guiomar G Peters Amy A Putman Tim T Rapp Christina K CK Rath Ana A Reese Justin J Rekerle Lauren L Roberts Angharad M AM Roy Suzy S Sanders Stephan J SJ Schuetz Catharina C Schulte Eva C EC Schulze Thomas G TG Schwarz Martin M Scott Katie K Seelow Dominik D Seitz Berthold B Shen Yiping Y Similuk Morgan N MN Simon Eric S ES Singh Balwinder B Smedley Damian D Smith Cynthia L CL Smolinsky Jake T JT Sperry Sarah S Stafford Elizabeth E Stefancsik Ray R Steinhaus Robin R Strawbridge Rebecca R Sundaramurthi Jagadish Chandrabose JC Talapova Polina P Tenorio Castano Jair A JA Tesner Pavel P Thomas Rhys H RH Thurm Audrey A Turnovec Marek M van Gijn Marielle E ME Vasilevsky Nicole A NA Vlčková Markéta M Walden Anita A Wang Kai K Wapner Ron R Ware James S JS Wiafe Addo A AA Wiafe Samuel A SA Wiggins Lisa D LD Williams Andrew E AE Wu Chen C Wyrwoll Margot J MJ Xiong Hui H Yalin Nefize N Yamamoto Yasunori Y Yatham Lakshmi N LN Yocum Anastasia K AK Young Allan H AH Yüksel Zafer Z Zandi Peter P PP Zankl Andreas A Zarante Ignacio I Zvolský Miroslav M Toro Sabrina S Carmody Leigh C LC Harris Nomi L NL Munoz-Torres Monica C MC Danis Daniel D Mungall Christopher J CJ Köhler Sebastian S Haendel Melissa A MA Robinson Peter N PN
Study Outcome
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Statistics
Citations : 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.Authors : 176
Identifiers
Doi : 10.1093/nar/gkad1005SSN : 1362-4962