{"id":"W4388616071","doi":"10.1093/nar/gkad1005","title":"The Human Phenotype Ontology in 2024: phenotypes around the world","year":2023,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":375,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Centre for Addiction and Mental Health; University of British Columbia; University of Toronto; Dalhousie University; Shriners Hospitals for Children - Canada; Simon Fraser University","funders":"National Institute of Dental and Craniofacial Research; National Institute of Child Health and Human Development; National Institute of Arthritis and Musculoskeletal and Skin Diseases; National Institute of Neurological Disorders and Stroke; National Institute of Mental Health; U.S. National Library of Medicine; Defense Advanced Research Projects Agency; McCusker Charitable Foundation; National Institutes of Health; Deutsche Forschungsgemeinschaft; Angela Wright Bennett Foundation; Berlin Institute of Health; National Center for Advancing Translational Sciences; National Human Genome Research Institute; Wellcome Trust; National Cancer Institute; British Heart Foundation; National Institute on Aging; Horizon 2020 Framework Programme; Eunice Kennedy Shriver National Institute of Child Health and Human Development; U.S. Department of Energy","keywords":"Ontology; Clinical phenotype; Biology; Inference; Phenotype; Data science; Disease; Analytics; Computer science; Computational biology; Bioinformatics; Artificial intelligence; Gene; Genetics; Medicine; Pathology","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001164989,0.0001102388,0.0001003492,0.0001236608,0.0007192934,0.0001079725,0.0007304523,0.00009064034,0.0000798955],"category_scores_gemma":[0.0002089025,0.00006638886,0.00006876539,0.000620165,0.0004449104,0.000002789431,0.0004655238,0.0003382157,0.0002781497],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003095159,"about_ca_system_score_gemma":0.0001226115,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001642617,"about_ca_topic_score_gemma":0.00431921,"domain_scores_codex":[0.9983269,0.0002797932,0.0001778554,0.000327398,0.0002796819,0.0006083559],"domain_scores_gemma":[0.9990228,0.0001497247,0.00002697946,0.0006113241,0.0001143801,0.00007472355],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0006076505,0.0003279299,0.05992437,0.00006829254,0.0002954808,0.0001809284,0.0009057836,0.0002957888,0.4036854,0.03687822,0.4465849,0.05024529],"study_design_scores_gemma":[0.0005917216,0.0002300436,0.1224166,0.00001709811,0.000009314981,0.000006162139,0.001906219,0.0003225243,0.003010184,0.008623718,0.8626266,0.0002398184],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9751639,0.001475495,0.00000279228,0.002871706,0.0002070122,0.0002703992,0.00001085799,0.00001495662,0.01998289],"genre_scores_gemma":[0.9759628,0.0004379134,0.000009590826,0.0001515457,0.0003924326,0.00006556829,0.00004385119,0.00002638661,0.02290992],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4160417,"threshold_uncertainty_score":0.5532296,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04171781329928882,"score_gpt":0.357094743870022,"score_spread":0.3153769305707332,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}