{"id":"W3215832582","doi":"10.1099/mgen.0.000728","title":"ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":131,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency; Public Health Agency of Canada","funders":"Public Health Agency of Canada","keywords":"In silico; Serotype; Escherichia coli; Whole genome sequencing; Computational biology; Genome; Sequence (biology); Biology; Genetics; Raw data; Microbiology; Gene; Mathematics; Statistics","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":[0.0002249988,0.0001632163,0.0002040659,0.00002830427,0.0001036966,0.00009148417,0.0002250461,0.0001415243,0.00001250066],"category_scores_gemma":[0.0001679971,0.0001799388,0.00002040325,0.0001201043,0.0001198758,0.00001300986,0.001086324,0.0001661759,0.000004122342],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000453979,"about_ca_system_score_gemma":0.0002197774,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001504587,"about_ca_topic_score_gemma":0.001435053,"domain_scores_codex":[0.9987505,0.0001166622,0.0001964211,0.000604634,0.00007146698,0.0002603339],"domain_scores_gemma":[0.9992656,0.00002746496,0.00004682618,0.0005080543,0.00007553981,0.00007648898],"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":[0.00007854935,0.00003588622,0.01570909,0.00002117268,0.00006786857,0.00001402258,0.0001334659,0.00003668056,0.9831778,0.000005620555,0.000500229,0.00021961],"study_design_scores_gemma":[0.002159289,0.000230872,0.1829716,0.00004234361,0.00006695461,0.00003458217,0.0005737812,0.001713228,0.4626658,0.00005778711,0.3488633,0.0006205071],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9942815,0.00408679,0.000138477,0.0002872197,0.0001229824,0.0001984991,0.0006982079,0.000009825036,0.0001764794],"genre_scores_gemma":[0.9869289,0.006823873,0.002641098,0.0002982749,0.0003257843,0.00001126813,0.002140292,0.000031207,0.0007992707],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.520512,"threshold_uncertainty_score":0.733769,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03759364213199561,"score_gpt":0.2697008992175524,"score_spread":0.2321072570855567,"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."}}