{"id":"W2055183967","doi":"10.3389/fcimb.2012.00057","title":"A Framework for Assessing the Concordance of Molecular Typing Methods and the True Strain Phylogeny of Campylobacter jejuni and C. coli Using Draft Genome Sequence Data","year":2012,"lang":"en","type":"article","venue":"Frontiers in Cellular and Infection Microbiology","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":32,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada; Canadian Food Inspection Agency; Health Canada","funders":"Public Health Agency of Canada; Government of Canada; Wellcome Trust","keywords":"Multilocus sequence typing; Campylobacter jejuni; Biology; Genetics; Whole genome sequencing; Typing; Phylogenetics; Phylogenetic tree; Computational biology; Genome; Genomics; Campylobacter coli; Comparative genomics; Locus (genetics); Molecular epidemiology; In silico; Concordance; Gene; Genotype","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":[0.001857519,0.0001227755,0.0003654802,0.00002068622,0.0001282051,0.00001700459,0.0001550397,0.0001793334,0.00000612567],"category_scores_gemma":[0.0002666464,0.00004845268,0.00004267248,0.0001433328,0.0007890853,0.0001068275,0.0001501112,0.0001529539,3.82488e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001552672,"about_ca_system_score_gemma":0.00001038983,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003159339,"about_ca_topic_score_gemma":0.00001742277,"domain_scores_codex":[0.9983681,0.000823146,0.0003043703,0.0002458588,0.00001778522,0.0002406786],"domain_scores_gemma":[0.9988239,0.0007432197,0.0002363074,0.0001204732,0.00004252094,0.00003353681],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00003552037,0.00001718139,0.06370681,0.00002300703,0.00003620992,1.364809e-7,0.0001733241,0.000005157503,0.9288871,0.001193847,0.000008599663,0.005913108],"study_design_scores_gemma":[0.005027056,0.00101332,0.678817,0.0004537375,0.0009068545,0.0006210341,0.007857239,0.01303922,0.1540501,0.07992199,0.05653413,0.001758366],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9166725,0.009040353,0.07334791,0.0001664227,0.0003613174,0.0002908518,0.0001056735,0.000004394533,0.00001054284],"genre_scores_gemma":[0.9732717,0.0006327922,0.02570034,0.0002386318,0.00008005412,0.000007652761,0.00006383925,0.000001755805,0.000003253358],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.774837,"threshold_uncertainty_score":0.2907418,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06379714226266163,"score_gpt":0.3433438433587934,"score_spread":0.2795467010961318,"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."}}