{"id":"W4304759114","doi":"10.3390/antibiotics11101400","title":"Three Distinct Annotation Platforms Differ in Detection of Antimicrobial Resistance Genes in Long-Read, Short-Read, and Hybrid Sequences Derived from Total Genomic DNA or from Purified Plasmid DNA","year":2022,"lang":"en","type":"article","venue":"Antibiotics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"U.S. Food and Drug Administration","keywords":"Biology; Plasmid; Resistome; genomic DNA; Enterococcus faecium; Genetics; DNA sequencing; Gene; Mobile genetic elements; Antibiotic resistance; Genome; Klebsiella pneumoniae; Microbiology; Escherichia coli; Bacteria","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":[0.001401922,0.00133794,0.0007975643,0.001214898,0.0005608537,0.001239478,0.0005982926,0.0008057212,0.001655324],"category_scores_gemma":[0.002165945,0.0006317123,0.001292979,0.001189291,0.0005192828,0.0007812075,0.001117483,0.0007324733,0.001883669],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003477502,"about_ca_system_score_gemma":0.0006274147,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000892164,"about_ca_topic_score_gemma":0.003201476,"domain_scores_codex":[0.997893,0.0003120597,0.0002796403,0.0007474431,0.0006092628,0.0001585075],"domain_scores_gemma":[0.9981399,0.0005167033,0.0003427379,0.0003070341,0.0005269313,0.0001668336],"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":[0.0005750694,0.00004732984,0.004639158,0.0007235584,0.0001443651,0.0001149319,0.0003651322,0.0005094813,0.9679056,0.0005943845,0.0005188996,0.02386204],"study_design_scores_gemma":[0.00005871428,0.0004007911,0.04400667,0.0001431852,0.0004060456,0.0007633895,0.0003532371,0.007901591,0.9166877,0.0007977481,0.02833803,0.0001428693],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6524994,0.003253767,0.2957602,0.00040155,0.0002746973,0.0007922199,0.02595875,0.008797789,0.01226154],"genre_scores_gemma":[0.3461704,0.001425448,0.5869312,0.0008926071,0.00005304964,0.001725576,0.05213807,0.001806292,0.008857415],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001655324,"threshold_uncertainty_score":0.007414103,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0119242682902536,"score_gpt":0.2277863727189761,"score_spread":0.2158621044287225,"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."}}