{"id":"W2153717161","doi":"10.1093/nar/gki593","title":"BASys: a web server for automated bacterial genome annotation","year":2005,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":319,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Genome Prairie; Genome Canada","keywords":"Annotation; Biology; Genome project; Computational biology; Web server; Gene Annotation; Genome; Bacterial genome size; Chromosome; GenBank; Gene; Genetics; Computer science; World Wide Web; The Internet","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005995385,0.0001231894,0.0001277106,0.00007632468,0.0002280316,0.00005720946,0.000250542,0.0001447939,0.00009895656],"category_scores_gemma":[0.0001243846,0.0001186516,0.00007772756,0.0001249658,0.0001035081,0.000001460254,0.0001852445,0.00008968863,0.00005891953],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003870501,"about_ca_system_score_gemma":0.0001272308,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001088836,"about_ca_topic_score_gemma":0.00005952126,"domain_scores_codex":[0.998708,0.0000897146,0.000189103,0.0003596791,0.0002087088,0.0004448542],"domain_scores_gemma":[0.9992247,0.00002842319,0.00003390277,0.0003153716,0.0003098314,0.00008779651],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001814396,0.00004963976,0.0004104248,0.00002013814,0.00005771837,5.200028e-7,0.000135494,0.00008519244,0.989481,0.00008169017,0.006533097,0.002963598],"study_design_scores_gemma":[0.001794064,0.0007588091,0.02393273,0.000008048535,0.00001319078,0.000006543874,0.0001936022,0.00431987,0.07615173,0.0001080489,0.8924234,0.0002899806],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.997087,0.0003870426,0.00004337553,0.0005622479,0.0001090011,0.000448977,0.0001507015,0.00001541027,0.001196219],"genre_scores_gemma":[0.9946073,0.0002030485,0.002757856,0.0001060215,0.0009948543,0.0001154682,0.0001773546,0.00003499069,0.001003146],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9133293,"threshold_uncertainty_score":0.4838473,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03681646007756522,"score_gpt":0.3313179337100662,"score_spread":0.294501473632501,"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."}}