The Human Phenotype Ontology in 2021

Journal Article · Wed Dec 02 00:00:00 EST 2020 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkaa1043· OSTI ID:1828340

Köhler, Sebastian ^[1]; Gargano, Michael ^[2]; Matentzoglu, Nicolas ^[3]; Carmody, Leigh C. ^[2]; Lewis-Smith, David ^[4]; Vasilevsky, Nicole A. ^[5]; Danis, Daniel; Balagura, Ganna ^[6]; Baynam, Gareth ^[7]; Brower, Amy M. ^[8]; Callahan, Tiffany J. ^[9]; Chute, Christopher G. ^[10]; Est, Johanna L. ^[11]; Galer, Peter D. ^[12]; Ganesan, Shiva ^[12]; Griese, Matthias ^[13]; Haimel, Matthias ^[14]; Pazmandi, Julia ^[15]; Hanauer, Marc ^[16]; Harris, Nomi L. ^[17] ; Hartnett, Michael J ^[8]; Hastreiter, Maximilian ^[11]; Hauck, Fabian ^[18]; He, Yongqun ^[19]; Jeske, Tim ^[11]; Kearney, Hugh ^[20]; Kindle, Gerhard ^[21]; Klein, Christoph ^[11]; Knoflach, Katrin ^[13]; Krause, Roland ^[22]; Lagorce, David ^[16]; McMurry, Julie A. ^[23]; Miller, Jillian A. ^[8]; Munoz-Torres, Monica C ^[23]; Peters, Rebecca L. ^[8]; Rapp, Christina K. ^[13]; Rath, Ana M. ^[16]; Rind, Shahmir A. ^[24]; Rosenberg, Avi Z ^[25]; Segal, Michael M. ^[26]; Seidel, Markus G. ^[27]; Smedley, Damian ^[28]; Talmy, Tomer ^[29]; Thomas, Yarlalu ^[30]; Wiafe, Samuel A. ^[31]; Xian, Julie ^[32]; Yüksel, Zafer ^[33]; Helbig, Ingo ^[34]; Mungall, Christopher J. ^[17]; Haendel, Melissa A. ^[35]; Robinson, Peter N. ^[36]

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1. Ada Health GmbH, Berlin, Germany; Monarch Initiative
2. Monarch Initiative; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
3. Monarch Initiative; Semanticly Ltd, London, UK; European Bioinformatics Institute (EMBL-EBI)
4. Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Clinical Neurosciences, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
5. Monarch Initiative; Oregon Clinical & Translational Research Institute, Oregon Health & Science University
6. Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS ‘G. Gaslini’ Institute, Genoa, Italy
7. Western Australian Register of Developmental Anomalies, King Edward memorial Hospital, Perth, Australia; Telethon Kids Institute and the Division of Paediatrics, Faculty of Helath and Medical Sciences, University of Western Australia, Perth, Australia
8. American College of Medical Genetics and Genomics (ACMG), Bethesda, MD, USA
9. Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Colorado, USA
10. Johns Hopkins University Schools of Medicine, Public Health, and Nursing
11. Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
12. Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Biomedical and Health Informatics (DBHi), Children's Hospital of Philadelphia, Philadelphia, PA, USA
13. Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Ludwig-Maximilians University, German Center for Lung Research (DZL), Munich, Germany
14. Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
15. Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
16. INSERM, US14––Orphanet, Plateforme Maladies Rares, Paris, France
17. Monarch Initiative; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley CA, USA
18. Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; German Centre for Infection Research (DZIF), Munich, Germany
19. 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
20. FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Ireland
21. Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI). Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany; Centre for Biobanking FREEZE, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
22. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
23. Monarch Initiative; Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA
24. WA Register of Developmental Anomalies; Curtin University, Western Australia, Australia
25. Division of Kidney-Urologic Pathology, Johns Hopkins University, Baltimore, MD 21205, USA
26. SimulConsult, Inc., Chestnut Hill, MA, USA
27. Research Unit for Pediatric Hematology and Immunology, Division of Pediatric Hemato-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
28. 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
29. Genomic Research Department, Emedgene Technologies, Tel Aviv, Israel; Faculty of Medicine, Hebrew University Hadassah Medical School, Jerusalem, Israel
30. West Australian Register of Developmental Anomalies, East Perth, WA, Australia
31. Rare Disease Ghana Initiative, Ghana
32. Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, PA, USA
33. Human Genetics, Bioscientia GmbH, Ingelheim, Germany
34. Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA; The Epilepsy NeuroGenetics Initiative (ENGIN), Children's Hospital of Philadelphia, Philadelphia, PA, USA
35. Monarch Initiative; Oregon Clinical & Translational Research Institute, Oregon Health & Science University; Translational and Integrative Sciences Center, Department of Environmental and Molecular Toxicology, Oregon State University, OR, USA
36. Monarch Initiative; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA

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.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: E-Rare-3; Monarch R24; NHGRI Phenomics; Solve-RD; USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Contributing Organization: HPO Team
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1828340
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 49; ISSN 0305-1048
• Publisher: Oxford University Press
• Country of Publication: United States
• Language: English

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59 BASIC BIOLOGICAL SCIENCES