{"id":"W2726286722","doi":"10.3389/fmicb.2017.01044","title":"The Validation and Implications of Using Whole Genome Sequencing as a Replacement for Traditional Serotyping for a National Salmonella Reference Laboratory","year":2017,"lang":"en","type":"article","venue":"Frontiers in Microbiology","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":86,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada; University of Manitoba","funders":"Government of Canada; Public Health Agency; Public Health Agency of Canada","keywords":"Salmonella; Serotype; Whole genome sequencing; Biology; DNA sequencing; Genome; Computational biology; Reference genome; Genetics; Microbiology; DNA; Gene; Bacteria","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"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":[0.09515232,0.001488524,0.001255547,0.001657441,0.00136341,0.005482126,0.003257378,0.002194708,0.0007461221],"category_scores_gemma":[0.1384749,0.0007355189,0.0009021551,0.002872091,0.00423095,0.002281795,0.001835814,0.002309081,0.0007589181],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.005237286,"about_ca_system_score_gemma":0.01032235,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.1341012,"about_ca_topic_score_gemma":0.1550912,"domain_scores_codex":[0.8907366,0.05372966,0.00542627,0.007854644,0.03969271,0.002560274],"domain_scores_gemma":[0.8633388,0.06335901,0.008869355,0.01635239,0.04599761,0.0020828],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.006549547,0.0009505029,0.4230848,0.003022859,0.001014057,0.001204002,0.008108472,0.02016613,0.207884,0.01331176,0.01196281,0.3027409],"study_design_scores_gemma":[0.0003536863,0.0101159,0.5575963,0.004328563,0.001550333,0.003214976,0.009622397,0.06257718,0.2433145,0.006363074,0.1001485,0.0008145472],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8370457,0.01158761,0.09699806,0.02815003,0.001919759,0.0008723328,0.002919772,0.0009183758,0.01958838],"genre_scores_gemma":[0.8764933,0.003703252,0.1082734,0.004767874,0.0001383384,0.0002139201,0.002035298,0.0002698564,0.004104845],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1341012,"threshold_uncertainty_score":0.5032196,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1094019887584561,"score_gpt":0.2968569704491046,"score_spread":0.1874549816906485,"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."}}