{"id":"W2607851825","doi":"10.1101/121350","title":"Plasmid Profiler: Comparative Analysis of Plasmid Content in WGS Data","year":2017,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Public Health Agency of Canada","funders":"","keywords":"Plasmid; Contig; Source code; Pipeline (software); Codebase; Software; Computer science; Open source; Biology; Computational biology; Database; Genome; Genetics; Operating system; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004504429,0.001200395,0.001445904,0.004301904,0.0008905186,0.002011779,0.001181725,0.0006628152,0.01679437],"category_scores_gemma":[0.007291742,0.0008999252,0.001567221,0.004038597,0.0004973472,0.001490031,0.001684713,0.001963484,0.01083204],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006187293,"about_ca_system_score_gemma":0.00107609,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001133091,"about_ca_topic_score_gemma":0.001360112,"domain_scores_codex":[0.9971113,0.0005293337,0.0003126592,0.0009628211,0.0008689567,0.0002149301],"domain_scores_gemma":[0.9965161,0.001480868,0.0006577363,0.0005593235,0.0005764368,0.0002095204],"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":[0.004069683,0.0003948416,0.02591603,0.005613019,0.001124526,0.001504826,0.002375274,0.007853014,0.5230408,0.005416392,0.1467254,0.2759662],"study_design_scores_gemma":[0.0004810333,0.001094764,0.1227799,0.0007454305,0.0005916742,0.00215409,0.0009846122,0.1448506,0.464107,0.009754187,0.2517277,0.0007289321],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.1276301,0.0009389548,0.5025523,0.0006289975,0.0003426166,0.0009140251,0.1851203,0.1740879,0.007784777],"genre_scores_gemma":[0.1376298,0.0005298938,0.658471,0.0002939983,0.00008223237,0.001510653,0.1678758,0.02949928,0.004107304],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01679437,"threshold_uncertainty_score":0.05618268,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07104185392618713,"score_gpt":0.2806856000835894,"score_spread":0.2096437461574023,"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."}}