{"id":"W4379184839","doi":"10.1371/journal.pone.0286728","title":"OntoTrek: 3D visualization of application ontology class hierarchies","year":2023,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Biomedical Text Mining and Ontologies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; Agricultural Research Service; Genome Canada; U.S. Department of Agriculture","keywords":"Visualization; Ontology; Class (philosophy); Computer science; Computational biology; Data science; World Wide Web; Evolutionary biology; Biology; Data mining; Artificial intelligence; Epistemology","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0001228652,0.0000744904,0.0001478248,0.00006908865,0.00003660389,0.000004067538,0.0001251067,0.0001583394,0.00001136278],"category_scores_gemma":[0.0002086028,0.0000706103,0.00003253266,0.0001739874,0.0001442424,0.000001337187,0.0000692878,0.00004321528,0.00003104836],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005828495,"about_ca_system_score_gemma":0.00002828856,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002019841,"about_ca_topic_score_gemma":0.00005353002,"domain_scores_codex":[0.999294,0.00004424865,0.0001682027,0.0002007707,0.0001390627,0.000153686],"domain_scores_gemma":[0.9995798,0.00002713975,0.00007355868,0.0002169376,0.00006577382,0.00003672486],"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":[0.00005543005,0.0002958003,0.006748602,0.00008086159,0.0001112032,7.05801e-7,0.00008984989,0.000003810913,0.975979,0.0006368543,0.0009219395,0.01507589],"study_design_scores_gemma":[0.0008902272,0.001202974,0.0383127,0.00009158432,0.0001131664,0.00000302697,0.0001992343,0.003521482,0.9299996,0.001081646,0.02424367,0.0003406501],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9937708,0.0003205104,0.003635714,0.0004340247,0.00003360243,0.000134162,0.00001569518,0.00008163493,0.001573888],"genre_scores_gemma":[0.9952912,0.0003541642,0.00261925,0.0001036015,0.0001163628,0.00005039199,0.000330722,0.0000126879,0.001121563],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0459794,"threshold_uncertainty_score":0.2879405,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03858406395107011,"score_gpt":0.2825247016146658,"score_spread":0.2439406376635956,"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."}}