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The Human Phenotype Ontology in 2024: phenotypes around the world

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Gargano, Michael A, Matentzoglu, Nicolas, Coleman, Ben, Addo-Lartey, Eunice B, Anagnostopoulos, Anna V, Anderton, Joel, Avillach, Paul, Bagley, Anita M +168 more·2024·Nucleic Acids Research
DOI 10.1093/nar/gkad1005PMC PMC10767975
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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.

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  • PhenoBERT is a state-of-the-art transformer-based model designed for phenotype extraction and normalization to HPO.

    “For this task, we adopted PhenoBERT23, a state-of-the-art transformer-based model designed for phenotype extraction and normalization to HPO35.”

    From TimeX: Phenotype Onset Extraction from Clinical Narratives (2026) · cites this paper as [35]

  • HPO incorporates information on phenotype onset from existing literature, but only 1.2% of the phenotypic abnormality annotations had onset information.

    “only 1.2% of the phenotypic abnormality annotations had onset information36”

    From TimeX: Phenotype Onset Extraction from Clinical Narratives (2026) · cites this paper as [36]

    The ‘Updates to the annotations’ section reports new HPO annotations and their literature citations, but gives no percentage with onset information. The ‘GA4GH phenopacket schema’ section says phenotypic observations can specify onset; it does not establish that 1.2% of HPO phenotypic-abnormality annotations did so. Searches for ‘1.2%’ and onset information found no supporting passage in our copy. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Gargano, M. A., Matentzoglu, N., Coleman, B., Addo-Lartey, E. B., Anagnostopoulos, A. V., Anderton, J., Avillach, P., Bagley, A. M., Bakštein, E., Balhoff, J. P., Baynam, G., Bello, S. M., Berk, M., Bertram, H., Bishop, S., Blau, H., Bodenstein, D. F., Botas, P., Boztug, K., Čady, J., Callahan, T. J., Cameron, R., Carbon, S. J., Castellanos, F., Caufield, J. H., Chan, L. E., Chute, C. G., Cruz-Rojo, J., Dahan-Oliel, N., Davids, J. R., de Dieuleveult, M., de Souza, V., de Vries, B. B. A., de Vries, E., DePaulo, J. R., Derfalvi, B., Dhombres, F., Diaz-Byrd, C., Dingemans, A. J. M., Donadille, B., Duyzend, M., Elfeky, R., Essaid, S., Fabrizzi, C., Fico, G., Firth, H. V., Freudenberg-Hua, Y., Fullerton, J. M., Gabriel, D. L., Gilmour, K., Giordano, J., Goes, F. S., Moses, R. G., Green, I., Griese, M., Groza, T., Gu, W., Guthrie, J., Gyori, B., Hamosh, A., Hanauer, M., Hanušová, K., He, Y. (., Hegde, H., Helbig, I., Holasová, K., Hoyt, C. T., Huang, S., Hurwitz, E., Jacobsen, J. O. B., Jiang, X., Joseph, L., Keramatian, K., King, B., Knoflach, K., Koolen, D. A., Kraus, M. L., Kroll, C., Kusters, M., Ladewig, M. S., Lagorce, D., Lai, M.-C., Lapunzina, P., Laraway, B., Lewis-Smith, D., Li, X., Lucano, C., Majd, M., Marazita, M. L., Martinez-Glez, V., McHenry, T. H., McInnis, M. G., McMurry, J. A., Mihulová, M., Millett, C. E., Mitchell, P. B., Moslerová, V., Narutomi, K., Nematollahi, S., Nevado, J., Nierenberg, A. A., Čajbiková, N. N., Nurnberger, J. I., Ogishima, S., Olson, D., Ortiz, A., Pachajoa, H., Perez de Nanclares, G., Peters, A., Putman, T., Rapp, C. K., Rath, A., Reese, J., Rekerle, L., Roberts, A. M., Roy, S., Sanders, S. J., Schuetz, C., Schulte, E. C., Schulze, T. G., Schwarz, M., Scott, K., Seelow, D., Seitz, B., Shen, Y., Similuk, M. N., Simon, E. S., Singh, B., Smedley, D., Smith, C. L., Smolinsky, J. T., Sperry, S., Stafford, E., Stefancsik, R., Steinhaus, R., Strawbridge, R., Sundaramurthi, J. C., Talapova, P., Tenorio Castano, J. A., Tesner, P., Thomas, R. H., Thurm, A., Turnovec, M., van Gijn, M. E., Vasilevsky, N. A., Vlčková, M., Walden, A., Wang, K., Wapner, R., Ware, J. S., Wiafe, A. A., Wiafe, S. A., Wiggins, L. D., Williams, A. E., Wu, C., Wyrwoll, M. J., Xiong, H., Yalin, N., Yamamoto, Y., Yatham, L. N., Yocum, A. K., Young, A. H., Yüksel, Z., Zandi, P. P., Zankl, A., Zarante, I., Zvolský, M., Toro, S., Carmody, L. C., Harris, N. L., Munoz-Torres, M. C., Danis, D., Mungall, C. J., Köhler, S., Haendel, M. A., & Robinson, P. N.
Affiliations
  • The Jackson Laboratory for Genomic Medicine (US)
  • Semanticly , Athens , Greece
  • Rare Disease Ghana Initiative (GH)
  • Jackson Laboratory (US)
  • University of Pittsburgh (US)
  • Harvard University (US)
  • Shriners Hospitals for Children - Northern California (US)
  • National Institute of Mental Health (CZ)
  • University of North Carolina at Chapel Hill (US)
  • Princess Margaret Hospital for Children (AU)
  • Barwon Health (AU)
  • University of Michigan (US)
  • University of California, San Francisco (US)
  • University of Toronto (CA)
  • Nostos Genomics GmbH , Berlin , Germany
  • St. Anna Children's Cancer Research Institute (CCRI) , Vienna , Austria
  • Institute of Health Information and Statistics (CZ)
  • Columbia University Irving Medical Center (US)
  • Simon Fraser University (CA)
  • Lawrence Berkeley National Laboratory (US)
  • Oregon State University (US)
  • Johns Hopkins University (US)
  • Hospital Universitario 12 De Octubre (ES)
  • 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  CB10 1SD , 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 Pediatrics, Dalhousie University , Halifax , NS , Canada
  • Inserm (FR)
  • Department of Psychiatry, University of Michigan , Ann Arbor , MI , USA
  • Radboud University Nijmegen (NL)
  • Massachusetts General Hospital (US)
  • University College London (GB)
  • University of Colorado Anschutz (US)
  • Centro de Investigación Biomédica en Red de Salud Mental (ES)
  • Addenbrooke's Hospital (GB)
  • Department of Psychiatry, Feinstein Institutes for Medical Research, Northwell Health, Manhasset , NY , USA
  • Neuroscience Research Australia (AU)
  • Great Ormond Street Hospital (GB)
  • National Institutes of Health (US)
  • SNOMED International , London  W2 6BD , UK
  • LMU Klinikum (DE)
  • Chinese HPO Consortium , Beijing , China
  • University of Vienna (AT)
  • Northeastern University (US)
  • Children's Hospital of Philadelphia (US)
  • Queen Mary University of London (GB)
  • University of British Columbia (CA)
  • Department of Ophthalmology, University Clinic Marburg - Campus Fulda , Fulda , Germany
  • Centre for Addiction and Mental Health (CA)
  • Hospital Universitario La Paz (ES)
  • Translational and Clinical Research Institute, Henry Wellcome Building, Framlington Place, Newcastle University , Newcastle-Upon-Tyne  NE14LP , UK
  • Brigham and Women's Hospital (US)
  • Center for Genomic Medicine, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí (I3PT-CERCA) , Sabadell , Spain
  • Charles University (CZ)
  • Northwell Health (US)
  • UNSW Sydney (AU)
  • Okinawa Prefectural Nanbu Medical Center & Children's Medical Center (JP)
  • McGill University (CA)
  • Institute of Medical and Molecular Genetics, Hospital Univ. La Paz , Madrid , Spain
  • Stark Neurosciences Research Institute, Departments of Psychiatry and Medical and Molecular Genetics, Indiana University School of Medicine , Indianapolis , IN , USA
  • Tohoku University (JP)
  • Critical Path Institute (US)
  • Universidad Icesi (CO)
  • Molecular (epi) genetics lab, Bioaraba Health Research Institute, Araba University Hospital , Vitoria-Gasteiz, Spain
  • MRC London Institute of Medical Sciences (GB)
  • University of Oxford (GB)
  • University Hospital Carl Gustav Carus (DE)
  • SUNY Upstate Medical University (US)
  • Dalhousie University (CA)
  • Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
  • Universitätsklinikum des Saarlandes (DE)
  • Mayo Clinic (US)
  • Rutgers, The State University of New Jersey (US)
  • National Alliance on Mental Illness (US)
  • European Bioinformatics Institute (GB)
  • King's College London (GB)
  • Tufts Medical Center (US)
  • Newcastle University (GB)
  • Department of Genetics, University Medical Center Groningen , Groningen , Netherlands
  • Department of Obstetrics and Gynecology, Columbia University Irving Medical Center , New York , NY , USA
  • Centers for Disease Control and Prevention (US)
  • MRC Centre for Regenerative Medicine (GB)
  • Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London , London , UK
  • Research Organization of Information and Systems (JP)
  • Department of Human Genetics, Bioscientia Healthcare GmbH , Ingelheim , Germany
  • The University of Sydney (AU)
  • Pontificia Universidad Javeriana (CO)
  • Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus , Aurora , CO  80045 , USA
  • The Jackson Laboratory for Genomic Medicine , Farmington , CT , USA
  • Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley , CA  94720 , USA
  • Ada Health GmbH , Berlin , Germany
Corresponding author
Robinson, Peter N
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2023-11-11
Volume
52
Issue
D1
Pages
D1333-D1346
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkad1005
PMC
PMC10767975
OpenAlex
W4388616071
Cited by
410
References
3
Citations by year
2026: 159 · 2025: 182 · 2024: 68 · 2023: 1
FWCI
36.42
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, cc-by)
  • IUScholarWorks (Indiana University) (submittedVersion, cc-by)
  • UNSWorks (University of New South Wales, Sydney, Australia) (submittedVersion, cc-by-nc-nd)
  • UCL Discovery (University College London) (submittedVersion, cc-by)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, other-oa)
  • Radboud Repository (Radboud University) (submittedVersion, other-oa)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • Kharkiv National Medical University Repository (Kharkiv National Medical University) (submittedVersion)
  • HAL (submittedVersion)
  • Figshare (submittedVersion, cc-by)
  • Research Portal (King's College London) (submittedVersion, cc-by)
  • The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion, cc-by)
  • Spiral (Imperial College London) (submittedVersion, other-oa)
  • Newcastle University ePrints (Newcastle Univesity) (cc-by)
Funders
  • NIH (5U24HG011449-03, 5R24OD011883-11, K08AG054727)
  • French Ministry of Health
  • NHGRI (7RM1HG010860-02)
  • NCATS (NCATS U24 TR002306)
  • Horizon 2020 (779257)
  • Defense Advanced Research Projects Agency (W911NF-20-1-0255)
  • DARPA Automating Scientific Knowledge Extraction and Modeling program (HR00112220036)
  • Berlin Institute of Health (CADS)
  • Wellcome Trust (203914/Z/16/Z)
  • Angela Wright Bennett Foundation
  • McCusker Charitable Foundation
  • Channel 7 Telethon Trusts
  • the Stan Perron Charitable Foundation and Mineral Resources
  • German Research Foundation (WY 215/1-1)
  • NLM (T15LM009451, NLM T15LM007079)
  • Canadian Institutes of Health Research Sex and Gender Science Chair (GSB 171373)
  • U.S. Department of Energy (DE-AC02-05CH11231)
  • NIMH (U24 MH068457)
  • NICHD (R01HD105266)
  • NIDCR (R03-DE032062)
  • Prechter Bipolar Research Program
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
Keywords
Human Phenotype Ontology, electronic health records, semantic similarity, psychiatric phenotypes, arthrogryposis
MeSH terms
Algorithms, Humans, Phenotype, Genomics, Rare Diseases, Biological Ontologies

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

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