{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.05122218,0.00259154,0.002073247,0.01312553,0.001593556,0.006378455,0.003638297,0.001973334,0.0007073568],"category_scores_gemma":[0.1161733,0.001345732,0.002966154,0.005219732,0.00454573,0.003585669,0.004816616,0.002589348,0.0002713351],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.004029714,"about_ca_system_score_gemma":0.005924598,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01317311,"about_ca_topic_score_gemma":0.007181225,"domain_scores_codex":[0.9583924,0.02393683,0.00405829,0.005401063,0.007294117,0.0009172377],"domain_scores_gemma":[0.9101609,0.0592681,0.01437587,0.005023242,0.01021863,0.0009532669],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0004352823,0.0004769393,0.06595881,0.00255835,0.001941524,0.001234504,0.002653556,0.4297353,0.0233308,0.192116,0.00370671,0.2758523],"study_design_scores_gemma":[0.00007738116,0.0006493459,0.01868811,0.0007178212,0.000395816,0.0005080994,0.0007568562,0.8173744,0.008420492,0.1418836,0.01025342,0.0002747268],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01644701,0.0005870612,0.9804296,0.0002879598,0.00003201486,0.0002371846,0.000357582,0.0007848475,0.0008368342],"genre_scores_gemma":[0.1023242,0.0002521099,0.8958856,0.00007896945,0.00002697504,0.0004708723,0.0007348002,0.0001103117,0.0001161097],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.05122218,"threshold_uncertainty_score":0.270892,"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."}}