{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001331283,0.0002525944,0.0005168769,0.0000252588,0.0002465097,0.0002013082,0.0002837752,0.0001171271,0.0003097739],"category_scores_gemma":[0.00009630949,0.0001108984,0.0002055264,0.0003702748,0.0001278594,0.00003887885,0.0002348163,0.000106053,0.00008112327],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003475158,"about_ca_system_score_gemma":0.00001197921,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008484398,"about_ca_topic_score_gemma":0.00116751,"domain_scores_codex":[0.9985027,0.0001120887,0.0003549617,0.0005467677,0.00009266109,0.000390873],"domain_scores_gemma":[0.9992381,0.0002056537,0.00009714873,0.00009449069,0.00004184366,0.0003227186],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001871995,0.0000313211,0.5151811,0.000009440931,0.0002598503,0.000004769393,0.0006316294,0.0002682139,0.47841,0.0002132208,0.001112296,0.003690979],"study_design_scores_gemma":[0.000145139,0.0002071066,0.9026988,0.000001906846,0.0002531201,0.000003375133,0.000378833,0.0008910377,0.002762784,0.0003545481,0.09194932,0.0003540831],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9952556,0.0003214855,0.0003003436,0.00342904,0.0001024825,0.0001833556,0.0001737346,0.00005731969,0.0001766719],"genre_scores_gemma":[0.9948748,0.0001510064,0.0006518132,0.003574039,0.0004325271,0.00000862794,0.0001412335,0.000002732559,0.0001632459],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4756472,"threshold_uncertainty_score":0.4522307,"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."}}