{"id":"W4316465996","doi":"10.3390/antibiotics12010175","title":"Studying the Association between Antibiotic Resistance Genes and Insertion Sequences in Metagenomes: Challenges and Pitfalls","year":2023,"lang":"en","type":"article","venue":"Antibiotics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Antibiotic resistance; Gene; Biology; Antibiotics; Genetics; Mobile genetic elements; Microbiome; Insertion sequence; Horizontal gene transfer; Computational biology; Plasmid; Genome; Transposable element","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":[0.02354007,0.00123311,0.002085134,0.003518202,0.001402451,0.004273576,0.001718044,0.001913137,0.001086448],"category_scores_gemma":[0.05324715,0.0008441174,0.001766339,0.006193233,0.002188788,0.00375518,0.002919284,0.002596896,0.000653723],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005746772,"about_ca_system_score_gemma":0.001551314,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003814625,"about_ca_topic_score_gemma":0.007946534,"domain_scores_codex":[0.9823344,0.008900395,0.002223838,0.003419766,0.002360581,0.0007610585],"domain_scores_gemma":[0.9349699,0.04354523,0.007501331,0.007991822,0.004578175,0.001413508],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.000784518,0.0002881355,0.7919183,0.007731892,0.004116824,0.0008787865,0.00275819,0.006206309,0.04308722,0.005349224,0.006939669,0.129941],"study_design_scores_gemma":[0.00008821344,0.0004401581,0.7900763,0.002560715,0.001880901,0.002265414,0.006858928,0.0313398,0.01846112,0.07654414,0.06919841,0.0002859689],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.6981885,0.07171618,0.1802,0.01985583,0.001458945,0.0004639306,0.02127812,0.0009906233,0.005847953],"genre_scores_gemma":[0.7867769,0.01115928,0.1864042,0.003775688,0.0008106196,0.000469792,0.009806735,0.0002995011,0.0004972999],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.02354007,"threshold_uncertainty_score":0.1244932,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03491184984266778,"score_gpt":0.2728605637665223,"score_spread":0.2379487139238545,"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."}}