{"id":"W3001915235","doi":"10.1101/2020.01.27.919118","title":"A <i>Vibrio cholerae</i> Core Genome Multilocus Sequence Typing Scheme to Facilitate the Epidemiological Study of Cholera","year":2020,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada; Centers for Disease Control and Prevention; Alberta Innovates; International Centre for Diarrhoeal Disease Research, Bangladesh; University of Oxford; University of Alberta; Canadian Institute for Advanced Research","keywords":"Multilocus sequence typing; Vibrio cholerae; Typing; Genome; Biology; Cholera; Outbreak; Genetics; Computational biology; Genotype; Virology; Gene; Bacteria","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001692292,0.0004524101,0.0003583323,0.00233156,0.0005772766,0.001063851,0.0006774428,0.0004371571,0.001471],"category_scores_gemma":[0.003690254,0.0001694875,0.0004944197,0.001677816,0.0004911132,0.0006004036,0.0008368375,0.000838885,0.0008985337],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008581873,"about_ca_system_score_gemma":0.001256486,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003221095,"about_ca_topic_score_gemma":0.004354052,"domain_scores_codex":[0.9988229,0.0003807878,0.0002201216,0.0002188168,0.0002492188,0.0001081048],"domain_scores_gemma":[0.9972831,0.0003565976,0.000705835,0.0005712963,0.000858705,0.0002245212],"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":[0.001985694,0.0005254656,0.2056546,0.0008119678,0.0002127238,0.0004758295,0.001189992,0.02175876,0.3817363,0.02334214,0.02977739,0.3325291],"study_design_scores_gemma":[0.000332531,0.002184478,0.3513534,0.0005405904,0.0002890148,0.002212987,0.0009095661,0.3292927,0.1155024,0.0166952,0.1802818,0.0004054254],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.4850513,0.000777369,0.4781574,0.0008455302,0.0005108386,0.002083342,0.0157212,0.005805602,0.01104722],"genre_scores_gemma":[0.3982538,0.0002204787,0.5839736,0.0002924374,0.0000642513,0.0006561125,0.01461442,0.0001912901,0.001733559],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.003221095,"threshold_uncertainty_score":0.008949816,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1095967897004757,"score_gpt":0.3039787221926662,"score_spread":0.1943819324921905,"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."}}