{"id":"W1980663822","doi":"10.1371/journal.pone.0122928","title":"GeneSippr: A Rapid Whole-Genome Approach for the Identification and Characterization of Foodborne Pathogens such as Priority Shiga Toxigenic Escherichia coli","year":2015,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":45,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency","funders":"Canadian Food Inspection Agency","keywords":"Biology; Whole genome sequencing; Genome; Computational biology; DNA sequencing; Multilocus sequence typing; Identification (biology); Typing; Genetics; Escherichia coli; Gene; Genotype","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":[0.00097338,0.001534947,0.0009302509,0.001195768,0.0006096195,0.001221317,0.000907076,0.001364081,0.001913643],"category_scores_gemma":[0.00101596,0.0007103785,0.001185209,0.001062406,0.0004071252,0.000956632,0.001270086,0.001410184,0.002568826],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004673583,"about_ca_system_score_gemma":0.0008858981,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001190985,"about_ca_topic_score_gemma":0.001920879,"domain_scores_codex":[0.9990175,0.0001128425,0.00007164707,0.0003172113,0.0003654602,0.0001153167],"domain_scores_gemma":[0.9995142,0.00009252355,0.0001134024,0.0001061862,0.0001116497,0.00006200279],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0004155483,0.00009679047,0.001904778,0.0005169117,0.00009064347,0.000264911,0.0001941953,0.0009975133,0.9514805,0.0005588116,0.005613148,0.03786623],"study_design_scores_gemma":[0.00009376994,0.0006940773,0.01884655,0.000101836,0.0001498507,0.001292505,0.0001821629,0.01131849,0.8871665,0.0009548485,0.07906009,0.0001392901],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.3661208,0.004081657,0.4828981,0.001412272,0.0006784135,0.002136144,0.0897968,0.03855043,0.01432533],"genre_scores_gemma":[0.2788031,0.003716747,0.5667623,0.001308583,0.0001368025,0.002349443,0.1240022,0.004946432,0.01797438],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.001913643,"threshold_uncertainty_score":0.006401777,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05448305085303085,"score_gpt":0.2612973514655063,"score_spread":0.2068143006124755,"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."}}