{"id":"W2902994010","doi":"10.1186/s12864-018-5243-3","title":"Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective","year":2018,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":72,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada; Canadian Food Inspection Agency","keywords":"Subtyping; Multiple Loci VNTR Analysis; VTEC; Outbreak; Whole genome sequencing; Biology; Public health surveillance; Multilocus sequence typing; Typing; Genome; Genetics; Computational biology; Public health; Virology; Escherichia coli; Medicine; Computer science; Tandem repeat; Genotype; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001104978,0.000119507,0.0001502079,0.00003994044,0.0002225011,0.00001595059,0.0002372404,0.0001193112,0.000007896924],"category_scores_gemma":[0.0008930096,0.0001058862,0.0001003472,0.0001173739,0.0002274076,0.000004122635,0.00008982927,0.00007138705,0.000003595266],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006454214,"about_ca_system_score_gemma":0.00220269,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.05659694,"about_ca_topic_score_gemma":0.6449808,"domain_scores_codex":[0.9988543,0.0001741938,0.0002125027,0.000268172,0.0002514503,0.0002393558],"domain_scores_gemma":[0.9978394,0.00005088532,0.0001510304,0.0003603703,0.0015299,0.00006841653],"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":[0.00009203793,0.00001139285,0.0006311808,0.000008437297,0.0001651769,3.556449e-8,0.001081136,0.000249064,0.9973457,0.00003685877,0.00003023425,0.0003487029],"study_design_scores_gemma":[0.001196836,0.0007162302,0.02816857,0.00001237218,0.0002538032,8.071854e-7,0.005769784,0.00639384,0.949741,0.001341008,0.006166517,0.000239243],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9949118,0.001060011,0.001944027,0.00007174962,0.0001179212,0.00101956,0.0002910468,0.000003543909,0.0005803241],"genre_scores_gemma":[0.9975289,0.00003558904,0.001757933,0.00005517789,0.0003736212,0.0001362204,0.00005217445,0.00002191972,0.00003851952],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5883839,"threshold_uncertainty_score":0.9496853,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05231302467533365,"score_gpt":0.3090712493718276,"score_spread":0.2567582246964939,"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."}}