{"id":"W2021074129","doi":"10.1371/journal.pone.0154556","title":"The Ontology for Biomedical Investigations","year":2016,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Biomedical Text Mining and Ontologies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":385,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Biotechnology and Biological Sciences Research Council; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Allergy and Infectious Diseases; Division of Biological Infrastructure; National Institute of General Medical Sciences; National Center for Advancing Translational Sciences; Agence Nationale de la Recherche; National Human Genome Research Institute; Engineering and Physical Sciences Research Council; National Institute on Drug Abuse; California Institute for Regenerative Medicine; National Institutes of Health; National Science Foundation","keywords":"Open Biomedical Ontologies; Ontology; Computer science; Process ontology; Data science; Upper ontology; Interoperability; Biological database; Ontology-based data integration; World Wide Web; Information retrieval; Semantic Web; Suggested Upper Merged Ontology; Bioinformatics; Biology","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":[0.0001584598,0.00006150189,0.00008250034,0.00001303515,0.0001343603,0.000007816837,0.0001765813,0.0001362198,0.00001031785],"category_scores_gemma":[0.001520392,0.00003075352,0.00003789287,0.00003461054,0.000549363,7.430325e-7,0.00005062208,0.00003200079,0.0000175539],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005981708,"about_ca_system_score_gemma":0.00005729014,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002093448,"about_ca_topic_score_gemma":0.00002616806,"domain_scores_codex":[0.9993924,0.00003042621,0.0001196629,0.0001631959,0.0000954065,0.0001988627],"domain_scores_gemma":[0.9994615,0.0001612182,0.00003468794,0.0002099019,0.00005322877,0.00007951315],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00005417187,0.0002583739,0.002250522,0.00001436081,0.0001922692,5.095176e-7,0.00001910566,1.117914e-8,0.9263481,0.001961359,0.021731,0.04717024],"study_design_scores_gemma":[0.001166038,0.001037182,0.002016947,0.0000724402,0.00006978335,0.000004785873,0.00005236978,0.00002757321,0.3182577,0.006869718,0.6702284,0.0001971366],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9102965,0.00139114,0.0200724,0.06634705,0.0002400936,0.0003995899,0.00008042732,0.00007764712,0.00109513],"genre_scores_gemma":[0.9603374,0.0005025449,0.02847454,0.001221037,0.0008380461,0.0003163222,0.00006662416,0.00002311733,0.008220353],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6484973,"threshold_uncertainty_score":0.2024151,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06034610189973234,"score_gpt":0.2676917707597481,"score_spread":0.2073456688600158,"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."}}