{"id":"W4223419307","doi":"10.1128/spectrum.00408-22","title":"Automated 16S Sequencing Using an R-Based Analysis Module for Bacterial Identification","year":2022,"lang":"en","type":"article","venue":"Microbiology Spectrum","topic":"Bacterial Identification and Susceptibility Testing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; Vancouver Coastal Health","funders":"","keywords":"Identification (biology); Sanger sequencing; 16S ribosomal RNA; Computational biology; DNA sequencing; Biology; Genetics; Gene; Ecology","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":[],"consensus_categories":[],"category_scores_codex":[0.0005740785,0.0001442241,0.0002011759,0.0001677704,0.0004675802,0.00005871904,0.0002648374,0.0001088245,0.0002568368],"category_scores_gemma":[0.0000721731,0.0001703724,0.0001665973,0.0003096939,0.00006557824,0.000007607915,0.00009212441,0.00007718757,0.000003487284],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001453853,"about_ca_system_score_gemma":0.0001611667,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001060413,"about_ca_topic_score_gemma":0.0002258439,"domain_scores_codex":[0.9984466,0.0002736714,0.0003632688,0.0005953597,0.00003904413,0.000282022],"domain_scores_gemma":[0.9991568,0.00001591574,0.0002105633,0.0004964157,0.00007051491,0.00004980537],"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":[0.00009587157,0.00008024223,0.002024538,0.000006968618,0.000121378,4.864124e-7,0.00002904766,0.00656649,0.9908637,0.00002346279,0.0001524114,0.00003534743],"study_design_scores_gemma":[0.0007252863,0.0002897441,0.004340881,0.000001514178,0.0002495015,0.00002433451,0.0001188367,0.09318039,0.897626,0.00005587137,0.003045642,0.0003419739],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9839939,0.00001944467,0.01445165,0.0001253608,0.0005239257,0.0003153913,0.0004460048,0.0001165044,0.000007753576],"genre_scores_gemma":[0.9880205,5.212946e-7,0.002575305,0.0001631366,0.0001739207,0.00005779866,0.0088583,0.00002273096,0.0001278173],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.09323773,"threshold_uncertainty_score":0.6947585,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02750825911848627,"score_gpt":0.2822799202147149,"score_spread":0.2547716610962287,"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."}}