{"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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0001573273,0.000271086,0.0003792086,0.0001056117,0.0001217604,0.00004276817,0.0002457241,0.0001480992,0.00003971934],"category_scores_gemma":[0.0000642283,0.0002609732,0.00006594615,0.0001665409,0.0002236051,0.00002314167,0.0002230448,0.0001825116,0.000001319593],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007988726,"about_ca_system_score_gemma":0.00009872735,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005388418,"about_ca_topic_score_gemma":0.01729354,"domain_scores_codex":[0.998234,0.00006243285,0.0005687865,0.0006234205,0.0001939928,0.0003173455],"domain_scores_gemma":[0.999261,0.00006548624,0.0002187344,0.0003608796,0.0000416487,0.00005227291],"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":[0.001121932,0.00008680162,0.2230326,0.0000358929,0.00004265236,0.00005099655,0.00007786988,0.00007456808,0.7744536,0.000003710694,0.00001738711,0.001001956],"study_design_scores_gemma":[0.0005508389,0.00009141815,0.499514,0.00004417668,0.00001951026,0.000009483886,0.0001091208,0.0001600593,0.4991884,0.00008187808,0.00002678336,0.0002043152],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9967163,0.0004580774,0.001295288,0.0000312776,0.0003169074,0.0003498278,0.0008009481,0.0000133108,0.00001805229],"genre_scores_gemma":[0.9977014,0.0002523726,0.000846329,0.00002999539,0.0001098763,0.000001894825,0.0009648313,0.00003793883,0.00005537356],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2764814,"threshold_uncertainty_score":0.9999843,"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."}}