{"id":"W2901332105","doi":"10.1093/nar/gky1105","title":"Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources","year":2018,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Biomedical Text Mining and Ontologies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":737,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ottawa Hospital; Children's Hospital of Eastern Ontario; University of Toronto; SickKids Foundation; University of Ottawa; Hospital for Sick Children","funders":"NHLBI Division of Intramural Research; National Center for Advancing Translational Sciences; National Human Genome Research Institute; British Heart Foundation; National Cancer Institute; National Institutes of Health; Horizon 2020; National Institute of Allergy and Infectious Diseases; Division of Intramural Research, National Institute of Allergy and Infectious Diseases; European Commission; National Institute for Health and Care Research; E-Rare","keywords":"Biology; Phenotype; Knowledge base; Ontology; Computational biology; Base (topology); Genetics; Gene; World Wide Web; Computer science; Epistemology","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":[0.0008154872,0.00008553639,0.0001253677,0.00006005958,0.0003081987,0.00001358442,0.0003940196,0.0002265391,0.00007710725],"category_scores_gemma":[0.0005609712,0.00005575241,0.00004099818,0.0001822957,0.002202622,0.000001644988,0.0005800861,0.0002099721,0.00001805109],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001013768,"about_ca_system_score_gemma":0.00007477729,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000714869,"about_ca_topic_score_gemma":0.0001659359,"domain_scores_codex":[0.9987067,0.0003105988,0.0001494316,0.0002912711,0.0002141415,0.0003278515],"domain_scores_gemma":[0.9991501,0.00005773216,0.00003597951,0.0004544613,0.0002185906,0.00008313981],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00009373759,0.00007257082,0.01096587,0.00003857505,0.00002662421,0.000001413552,0.001039025,4.948866e-8,0.9144443,0.0004016357,0.01280014,0.06011607],"study_design_scores_gemma":[0.001152777,0.002742946,0.1477737,0.0001035143,0.00001730169,0.00001993446,0.001694491,0.0001094578,0.4254525,0.001420615,0.4192579,0.0002548414],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9895969,0.001161664,0.00004086863,0.000454809,0.00008824204,0.00009698996,0.000004461678,0.00001028162,0.008545777],"genre_scores_gemma":[0.9974517,0.00005201823,0.0004061405,0.00006039156,0.0002777966,0.000006945616,0.000003709517,0.00001214094,0.001729207],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4889918,"threshold_uncertainty_score":0.8115653,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05771103562546586,"score_gpt":0.3712816491888905,"score_spread":0.3135706135634246,"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."}}