{"id":"W2743821210","doi":"10.1101/173146","title":"chewBBACA: A complete suite for gene-by-gene schema creation and strain identification","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":100,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Public Health Agency; Public Health Agency of Canada","keywords":"Computer science; Suite; Genome; File format; Software suite; Software; Directory; Source code; Computational biology; Database; Gene; Biology; Genetics; Programming language; Operating system","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004309359,0.004347256,0.00306005,0.003346598,0.001433148,0.005034014,0.004879169,0.001898417,0.08383591],"category_scores_gemma":[0.01383005,0.003128363,0.004222189,0.00245352,0.0006630443,0.003099268,0.004942957,0.004879577,0.09193365],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0010321,"about_ca_system_score_gemma":0.003492996,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003437207,"about_ca_topic_score_gemma":0.005619029,"domain_scores_codex":[0.9975181,0.0004420812,0.000357106,0.0005386399,0.0008891238,0.0002550749],"domain_scores_gemma":[0.9961572,0.001661182,0.0003968019,0.0007967398,0.0006921892,0.0002959236],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.000653912,0.0001368368,0.002960715,0.003436132,0.0005806455,0.0006721703,0.0004314159,0.002618893,0.0205452,0.005043852,0.8546906,0.1082296],"study_design_scores_gemma":[0.0005838661,0.0001848861,0.005650102,0.0009776504,0.0002437041,0.00160566,0.000215989,0.03394812,0.03805988,0.01942866,0.8986107,0.0004908421],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.003558435,0.001965855,0.1794958,0.0004963901,0.0003839646,0.0007013928,0.1081659,0.6954755,0.009756736],"genre_scores_gemma":[0.01896722,0.002497706,0.3346897,0.001631958,0.0001213624,0.002719708,0.3569007,0.2698936,0.01257815],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.08383591,"threshold_uncertainty_score":0.280459,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02003474481077103,"score_gpt":0.2438190952378011,"score_spread":0.22378435042703,"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."}}