{"id":"W2557385283","doi":"10.1093/nar/gkw1039","title":"The Human Phenotype Ontology in 2017","year":2016,"lang":"en","type":"review","venue":"Nucleic Acids Research","topic":"Biomedical Text Mining and Ontologies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":801,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; University of Toronto; Children's Hospital of Eastern Ontario; Hospital for Sick Children; University of Ottawa","funders":"Basic Energy Sciences; U.S. National Library of Medicine; Office of Science; National Institute for Health and Care Research; Bundesministerium für Bildung und Forschung; U.S. Department of Energy; European Commission; National Institutes of Health; NIHR Biomedical Research Centre, Royal Marsden NHS Foundation Trust/Institute of Cancer Research; Deutsche Forschungsgemeinschaft; Moorfields Eye Hospital NHS Foundation Trust; European Science Foundation; Cold Spring Harbor Laboratory; British Heart Foundation; National Human Genome Research Institute; Wellcome Trust; E-Rare","keywords":"Phenotype; Biology; Computational biology; Ontology; Clinical phenotype; Terminology; Pipeline (software); Disease; Bioinformatics; Controlled vocabulary; Data science; Genetics; Computer science; Gene; Information retrieval; Pathology; Medicine","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":[0.002192489,0.0002715722,0.0006641307,0.0001713512,0.000409123,0.00006063083,0.001494727,0.001014176,0.00007123164],"category_scores_gemma":[0.00112745,0.0001439199,0.0002257919,0.0002542263,0.001324475,0.000001548669,0.0007394883,0.0009193275,0.0004255885],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008408828,"about_ca_system_score_gemma":0.0004259975,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003941078,"about_ca_topic_score_gemma":0.0002117504,"domain_scores_codex":[0.9966519,0.0009614939,0.0004530075,0.0006369021,0.0004018558,0.0008948804],"domain_scores_gemma":[0.9982564,0.0003568596,0.0001083118,0.001034194,0.0001186826,0.0001255674],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0000114547,0.00002753678,0.00001770785,0.0004071484,0.00005518419,0.00002013968,0.00001241038,3.527427e-9,0.0001105542,0.0004248391,0.02772427,0.9711888],"study_design_scores_gemma":[0.0001891193,0.0002353257,0.00004839002,0.001156231,0.00001221158,0.00001908952,0.00002817056,2.70319e-7,0.000009710996,0.0003834789,0.9977339,0.0001841166],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0001143846,0.9886777,0.00001433523,0.0002981502,0.0002143089,0.0003588687,0.00001832699,0.00001639365,0.01028757],"genre_scores_gemma":[0.0002063518,0.9907259,0.000073583,0.00002170046,0.0005426283,0.0001461799,0.00005399193,0.0000457414,0.008183876],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9710047,"threshold_uncertainty_score":0.7822254,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1460962601911709,"score_gpt":0.4624024800580583,"score_spread":0.3163062198668875,"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."}}