{"id":"W3032654237","doi":"10.1186/s12864-020-06780-y","title":"Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries","year":2020,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":51,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph; McGill University; Ste. Anne's Hospital; Université Laval; Health Canada","funders":"Ontario Ministry of Research and Innovation; Health Canada; Genome British Columbia; Génome Québec; Genome Canada","keywords":"Biology; Citrobacter; Salmonella enterica; Salmonella; Genetics; Genome; Population; Phylogenetic tree; Evolutionary biology; Computational biology; Gene; Enterobacteriaceae; Escherichia coli; 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":[0.000581375,0.0003938274,0.0003971234,0.003259305,0.000574664,0.0008374702,0.0003079491,0.0004357369,0.002642537],"category_scores_gemma":[0.000973095,0.0001455743,0.0007971131,0.003006496,0.0002762266,0.0004452263,0.0006720796,0.0006050469,0.00071295],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004605266,"about_ca_system_score_gemma":0.0004923848,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002347951,"about_ca_topic_score_gemma":0.002505982,"domain_scores_codex":[0.9996285,0.00006112214,0.00002858924,0.0001396154,0.00005172766,0.00009036903],"domain_scores_gemma":[0.9993939,0.0001508042,0.0001751493,0.00004704119,0.0001053225,0.0001277519],"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":[0.001689691,0.0005546116,0.3854363,0.001156508,0.0005682684,0.0007526937,0.001701106,0.002848682,0.5381249,0.00178013,0.001573632,0.06381346],"study_design_scores_gemma":[0.00004492519,0.0004501996,0.9504436,0.0001471399,0.0003178234,0.001307539,0.002018536,0.01432318,0.0154675,0.002027258,0.01340828,0.00004394275],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9799935,0.001180484,0.008842136,0.0002344275,0.00002092524,0.0001389301,0.006516037,0.0001328664,0.002940677],"genre_scores_gemma":[0.9538367,0.0005381588,0.02893489,0.0001882671,0.00001709564,0.0001349871,0.01545697,0.00009501079,0.0007980201],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003259305,"threshold_uncertainty_score":0.008840203,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04790101113987598,"score_gpt":0.2232177705908209,"score_spread":0.1753167594509449,"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."}}