{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T18:52:18Z","timestamp":1775933538113,"version":"3.50.1"},"reference-count":67,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,12,2]],"date-time":"2020-12-02T00:00:00Z","timestamp":1606867200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Monarch R24","award":["2R24OD011883-05A1"],"award-info":[{"award-number":["2R24OD011883-05A1"]}]},{"DOI":"10.13039\/100000051","name":"NHGRI","doi-asserted-by":"publisher","award":["1RM1HG010860"],"award-info":[{"award-number":["1RM1HG010860"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NHGRI\/NCI","award":["5U13CA221044"],"award-info":[{"award-number":["5U13CA221044"]}]},{"name":"Solve-RD","award":["779257"],"award-info":[{"award-number":["779257"]}]},{"name":"HIPBI","award":["643578"],"award-info":[{"award-number":["643578"]}]},{"DOI":"10.13039\/501100001659","name":"DFG","doi-asserted-by":"publisher","award":["Gr 970\/9-1"],"award-info":[{"award-number":["Gr 970\/9-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"E-Rare-3"},{"name":"HCQ4Surfdefect"},{"name":"Cost CA","award":["16125 ENTeR-chILD"],"award-info":[{"award-number":["16125 ENTeR-chILD"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Human Phenotype Ontology (HPO, https:\/\/hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail.We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1043","type":"journal-article","created":{"date-parts":[[2020,11,16]],"date-time":"2020-11-16T15:17:13Z","timestamp":1605539833000},"page":"D1207-D1217","source":"Crossref","is-referenced-by-count":1066,"title":["The Human Phenotype Ontology in 2021"],"prefix":"10.1093","volume":"49","author":[{"given":"Sebastian","family":"K\u00f6hler","sequence":"first","affiliation":[{"name":"Ada Health GmbH, Berlin, Germany"},{"name":"Monarch Initiative"}]},{"given":"Michael","family":"Gargano","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA"}]},{"given":"Nicolas","family":"Matentzoglu","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"Semanticly Ltd, London, UK"},{"name":"European Bioinformatics Institute (EMBL-EBI)"}]},{"given":"Leigh C","family":"Carmody","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA"}]},{"given":"David","family":"Lewis-Smith","sequence":"additional","affiliation":[{"name":"Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK"},{"name":"Clinical Neurosciences, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK"}]},{"given":"Nicole A","family":"Vasilevsky","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"Oregon Clinical & Translational Research Institute, Oregon Health & Science University"}]},{"given":"Daniel","family":"Danis","sequence":"additional","affiliation":[]},{"given":"Ganna","family":"Balagura","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, Genoa, Italy"},{"name":"Pediatric Neurology and Muscular Diseases Unit, IRCCS \u2018G. Gaslini\u2019 Institute, Genoa, Italy"}]},{"given":"Gareth","family":"Baynam","sequence":"additional","affiliation":[{"name":"Western Australian Register of Developmental Anomalies, King Edward memorial Hospital, Perth, Australia"},{"name":"Telethon Kids Institute and the Division of Paediatrics, Faculty of Helath and Medical Sciences, University of Western Australia, Perth, Australia"}]},{"given":"Amy M","family":"Brower","sequence":"additional","affiliation":[{"name":"American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA"}]},{"given":"Tiffany J","family":"Callahan","sequence":"additional","affiliation":[{"name":"Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Colorado, USA"}]},{"given":"Christopher G","family":"Chute","sequence":"additional","affiliation":[{"name":"Johns Hopkins University Schools of Medicine, Public Health, and Nursing"}]},{"given":"Johanna L","family":"Est","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"}]},{"given":"Peter D","family":"Galer","sequence":"additional","affiliation":[{"name":"Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA"},{"name":"Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA"}]},{"given":"Shiva","family":"Ganesan","sequence":"additional","affiliation":[{"name":"Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA"},{"name":"Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA"}]},{"given":"Matthias","family":"Griese","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"},{"name":"Ludwig-Maximilians University, German Center for Lung Research (DZL), Munich, Germany"}]},{"given":"Matthias","family":"Haimel","sequence":"additional","affiliation":[{"name":"Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria"},{"name":"CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria"}]},{"given":"Julia","family":"Pazmandi","sequence":"additional","affiliation":[{"name":"Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria"},{"name":"CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria"},{"name":"Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA"}]},{"given":"Marc","family":"Hanauer","sequence":"additional","affiliation":[{"name":"INSERM, US14\u2013\u2013Orphanet, Plateforme Maladies Rares, Paris, France"}]},{"given":"Nomi L","family":"Harris","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley CA, USA"}]},{"given":"Michael\u00a0J","family":"Hartnett","sequence":"additional","affiliation":[{"name":"American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA"}]},{"given":"Maximilian","family":"Hastreiter","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"}]},{"given":"Fabian","family":"Hauck","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"},{"name":"German Centre for Infection Research (DZIF), Munich, Germany"}]},{"given":"Yongqun","family":"He","sequence":"additional","affiliation":[{"name":"Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA"}]},{"given":"Tim","family":"Jeske","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"}]},{"given":"Hugh","family":"Kearney","sequence":"additional","affiliation":[{"name":"FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Ireland"}]},{"given":"Gerhard","family":"Kindle","sequence":"additional","affiliation":[{"name":"Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI). Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany"},{"name":"Centre for Biobanking FREEZE, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany"}]},{"given":"Christoph","family":"Klein","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"}]},{"given":"Katrin","family":"Knoflach","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"},{"name":"Ludwig-Maximilians University, German Center for Lung Research (DZL), Munich, Germany"}]},{"given":"Roland","family":"Krause","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg"}]},{"given":"David","family":"Lagorce","sequence":"additional","affiliation":[{"name":"INSERM, US14\u2013\u2013Orphanet, Plateforme Maladies Rares, Paris, France"}]},{"given":"Julie A","family":"McMurry","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA"}]},{"given":"Jillian A","family":"Miller","sequence":"additional","affiliation":[{"name":"American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA"}]},{"given":"Monica\u00a0C","family":"Munoz-Torres","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA"}]},{"given":"Rebecca L","family":"Peters","sequence":"additional","affiliation":[{"name":"American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA"}]},{"given":"Christina K","family":"Rapp","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany"},{"name":"Ludwig-Maximilians University, German Center for Lung Research (DZL), Munich, Germany"}]},{"given":"Ana M","family":"Rath","sequence":"additional","affiliation":[{"name":"INSERM, US14\u2013\u2013Orphanet, Plateforme Maladies Rares, Paris, France"}]},{"given":"Shahmir A","family":"Rind","sequence":"additional","affiliation":[{"name":"WA Register of Developmental Anomalies"},{"name":"Curtin University, Western Australia, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2356-950X","authenticated-orcid":false,"given":"Avi\u00a0Z","family":"Rosenberg","sequence":"additional","affiliation":[{"name":"Division of Kidney-Urologic Pathology, Johns Hopkins University, Baltimore, MD 21205, USA"}]},{"given":"Michael M","family":"Segal","sequence":"additional","affiliation":[{"name":"SimulConsult, Inc., Chestnut Hill, MA,\u00a0USA"}]},{"given":"Markus G","family":"Seidel","sequence":"additional","affiliation":[{"name":"Research Unit for Pediatric Hematology and Immunology, Division of Pediatric Hemato-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria"}]},{"given":"Damian","family":"Smedley","sequence":"additional","affiliation":[{"name":"The William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ, UK"}]},{"given":"Tomer","family":"Talmy","sequence":"additional","affiliation":[{"name":"Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel"},{"name":"Faculty of Medicine, Hebrew University Hadassah Medical School, Jerusalem, Israel"}]},{"given":"Yarlalu","family":"Thomas","sequence":"additional","affiliation":[{"name":"West Australian Register of Developmental Anomalies, East Perth, WA, Australia"}]},{"given":"Samuel A","family":"Wiafe","sequence":"additional","affiliation":[{"name":"Rare Disease Ghana Initiative, Ghana"}]},{"given":"Julie","family":"Xian","sequence":"additional","affiliation":[{"name":"Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA"},{"name":"The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, PA, USA"}]},{"given":"Zafer","family":"Y\u00fcksel","sequence":"additional","affiliation":[{"name":"Human Genetics, Bioscientia GmbH, Ingelheim, Germany"}]},{"given":"Ingo","family":"Helbig","sequence":"additional","affiliation":[{"name":"Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA"},{"name":"The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA"}]},{"given":"Christopher J","family":"Mungall","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley CA, USA"}]},{"given":"Melissa A","family":"Haendel","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"Oregon Clinical & Translational Research Institute, Oregon Health & Science University"},{"name":"Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0736-9199","authenticated-orcid":false,"given":"Peter N","family":"Robinson","sequence":"additional","affiliation":[{"name":"Monarch Initiative"},{"name":"The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA"},{"name":"Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,12,2]]},"reference":[{"key":"2021010313131735700_B1","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/j.ajhg.2008.09.017","article-title":"The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease","volume":"83","author":"Robinson","year":"2008","journal-title":"Am. J. Hum. Genet."},{"key":"2021010313131735700_B2","doi-asserted-by":"crossref","first-page":"D966","DOI":"10.1093\/nar\/gkt1026","article-title":"The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data","volume":"42","author":"K\u00f6hler","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2021010313131735700_B3","doi-asserted-by":"crossref","first-page":"D865","DOI":"10.1093\/nar\/gkw1039","article-title":"The Human Phenotype Ontology in 2017","volume":"45","author":"K\u00f6hler","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313131735700_B4","doi-asserted-by":"crossref","first-page":"D1018","DOI":"10.1093\/nar\/gky1105","article-title":"Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources","volume":"47","author":"K\u00f6hler","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021010313131735700_B5","first-page":"41","article-title":"Coverage of phenotypes in standard terminologies","volume-title":"Proceedings of the Joint BioOntologies and BioLINK ISMB\u20192014 SIG session \u2018Phenotype Day.\u2019","author":"Rainer","year":"2014"},{"key":"2021010313131735700_B6","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1056\/NEJMra1615014","article-title":"Classification, ontology, and precision medicine","volume":"379","author":"Haendel","year":"2018","journal-title":"N. Engl. J. Med."},{"key":"2021010313131735700_B7","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.2656","article-title":"eXtasy: variant prioritization by genomic data fusion","volume":"10","author":"Sifrim","year":"2013","journal-title":"Nat. Methods"},{"key":"2021010313131735700_B8","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nmeth.3046","article-title":"Phen-Gen: combining phenotype and genotype to analyze rare disorders","volume":"11","author":"Javed","year":"2014","journal-title":"Nat. Methods"},{"key":"2021010313131735700_B9","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1016\/j.ajhg.2014.03.010","article-title":"Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families","volume":"94","author":"Singleton","year":"2014","journal-title":"Am. J. Hum. Genet."},{"key":"2021010313131735700_B10","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41591-018-0279-0","article-title":"Identifying facial phenotypes of genetic disorders using deep learning","volume":"25","author":"Gurovich","year":"2019","journal-title":"Nat. Med."},{"key":"2021010313131735700_B11","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1002\/humu.22851","article-title":"PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases","volume":"36","author":"Buske","year":"2015","journal-title":"Hum. Mutat."},{"key":"2021010313131735700_B12","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1136\/jnnp.2004.040451","article-title":"Simulconsult: www.simulconsult.com","volume":"76","author":"Fuller","year":"2005","journal-title":"J. Neurol. Neurosurg. 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