{"id":"W2992116856","doi":"10.1186/s12864-019-6259-z","title":"Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: divergence and speciation","year":2019,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"National Natural Science Foundation of China","keywords":"Biology; Genetics; Phylogenetic tree; Pathogenicity island; Phylogenetics; Salmonella; Evolutionary biology; Gene; Genome; Lineage (genetic)","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0002157266,0.0003416725,0.0003139326,0.0009852186,0.0004574077,0.0003916505,0.0002697439,0.000554883,0.001236744],"category_scores_gemma":[0.0003713143,0.0001579478,0.0002527543,0.000574804,0.0003845162,0.0002457708,0.0006946645,0.0004029678,0.0002341157],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004234732,"about_ca_system_score_gemma":0.0003387628,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001925149,"about_ca_topic_score_gemma":0.00274031,"domain_scores_codex":[0.9998084,0.00003176152,0.00001184394,0.00005356182,0.00003013767,0.00006442154],"domain_scores_gemma":[0.9997812,0.00004787669,0.00007237835,0.00001770136,0.00003397213,0.00004690185],"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":[0.002044484,0.0001251604,0.2776064,0.000329818,0.00007770202,0.0008298022,0.002071423,0.0006434218,0.685654,0.0009440414,0.0001435899,0.02953015],"study_design_scores_gemma":[0.00003021278,0.0007458424,0.9568751,0.00010149,0.00007147183,0.003554464,0.002998451,0.001908786,0.02909459,0.0007099212,0.003870919,0.00003881678],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9986488,0.0003177054,0.0004191378,0.0000302201,0.000003852262,0.00001333973,0.0001211487,0.000006098201,0.0004398106],"genre_scores_gemma":[0.9982261,0.00013637,0.00106537,0.00002668777,0.000003888975,0.0000113737,0.0003612564,0.000004334446,0.0001646044],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001925149,"threshold_uncertainty_score":0.004137278,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01609277222035931,"score_gpt":0.2249188989457362,"score_spread":0.2088261267253769,"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."}}