{"id":"W2394763400","doi":"10.1371/journal.pone.0147101","title":"The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies","year":2016,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":605,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada; Government of Canada; Canadian Food Inspection Agency","keywords":"Subtyping; Multilocus sequence typing; In silico; Genome; Biology; Context (archaeology); Typing; Whole genome sequencing; Computational biology; Salmonella; Phylogenetic tree; Genetics; Database; Computer science; Gene","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":[0.001618197,0.0002574816,0.0004933451,0.00003205672,0.0005829614,0.0003336667,0.00091628,0.0001862514,0.00006919675],"category_scores_gemma":[0.0005114186,0.00009368149,0.00006343341,0.0002981458,0.000160678,0.0003981508,0.0004270931,0.0001531484,0.00002161256],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000562413,"about_ca_system_score_gemma":0.00002472116,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001275689,"about_ca_topic_score_gemma":0.0007243797,"domain_scores_codex":[0.9976009,0.0003693923,0.0005313966,0.0006719101,0.0001370773,0.0006893662],"domain_scores_gemma":[0.9973009,0.002036405,0.0002223978,0.0002127464,0.00008456317,0.0001429599],"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":[0.0003099177,0.0002222369,0.08066796,0.00002620452,0.00005516789,0.000001938799,0.00009009979,0.000001432613,0.8923753,0.0003784978,0.0001105161,0.02576066],"study_design_scores_gemma":[0.001471624,0.00103583,0.9443172,0.0005937407,0.00009942301,0.00001360889,0.001182906,0.0006090619,0.01559948,0.004772972,0.02923512,0.001069074],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9929829,0.001299213,0.000009788457,0.003845,0.00004337738,0.0008108599,0.00003102114,0.00007696157,0.0009009335],"genre_scores_gemma":[0.997019,0.0008379627,0.0003196598,0.0004888911,0.0003602802,0.0001610858,0.00003057205,0.000007012818,0.0007755412],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8767759,"threshold_uncertainty_score":0.4483726,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07572463021093476,"score_gpt":0.2695500370457397,"score_spread":0.193825406834805,"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."}}