{"id":"W2800439744","doi":"10.3389/fmicb.2018.00836","title":"Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping","year":2018,"lang":"en","type":"article","venue":"Frontiers in Microbiology","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":62,"is_retracted":false,"has_abstract":true,"ca_institutions":"Wilfrid Laurier University; Public Health Agency of Canada; Institut National de Santé Publique du Québec; Health Canada; Université de Montréal; Université Laval; McGill University; Canadian Food Inspection Agency","funders":"Canadian Food Inspection Agency; Public Health Agency of Canada; Genome Canada","keywords":"Prophage; Subtyping; Biology; Salmonella enterica; Salmonella; Genome; Genetics; Serotype; Typing; Microbiology; Gene; Bacteriophage; Bacteria; Escherichia coli","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":[0.0005242781,0.0005897481,0.0004237403,0.00291831,0.0001753704,0.0008331338,0.0001563375,0.0004066661,0.001405774],"category_scores_gemma":[0.001391653,0.0002501042,0.000331705,0.00196038,0.0002603167,0.0004231096,0.0004692533,0.0004415528,0.0007522316],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001266441,"about_ca_system_score_gemma":0.0001096112,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000620511,"about_ca_topic_score_gemma":0.0008783286,"domain_scores_codex":[0.9996637,0.00007223112,0.00003028499,0.0000956219,0.00009809156,0.00004009283],"domain_scores_gemma":[0.9987713,0.0004995994,0.00041132,0.00007951666,0.0001442596,0.00009397926],"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":[0.0006403313,0.0001188456,0.2055703,0.0005422297,0.0002308286,0.000217305,0.0003266378,0.001004533,0.7436824,0.0001848041,0.000325868,0.04715579],"study_design_scores_gemma":[0.000008268149,0.0004369617,0.9353665,0.00006820403,0.0001296784,0.0006488935,0.000407208,0.003772418,0.05664524,0.0004064302,0.002082379,0.00002793403],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9814122,0.002038756,0.01037102,0.00005747205,0.00001642685,0.00004122922,0.004336569,0.0001946228,0.001531753],"genre_scores_gemma":[0.9756966,0.001256578,0.01707121,0.00004812281,0.00001472924,0.00004848628,0.00526876,0.00004319934,0.0005522796],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00291831,"threshold_uncertainty_score":0.004702806,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04196211225866381,"score_gpt":0.2524054734833197,"score_spread":0.2104433612246559,"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."}}