{"id":"W4410007634","doi":"10.1093/nar/gkaf360","title":"BASys2: a next-generation bacterial genome annotation system","year":2025,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Genome Alberta; Canada Foundation for Innovation; Genome Canada","keywords":"Biology; Annotation; Genome; Bacterial genome size; Computational biology; Genetics; Genome project; Gene","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":[0.002126181,0.002536519,0.001870688,0.002201463,0.001452938,0.002336353,0.002781992,0.001452858,0.01609235],"category_scores_gemma":[0.001857215,0.001217238,0.001539962,0.001935962,0.0003586742,0.001802307,0.002449198,0.002380717,0.03225988],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00107073,"about_ca_system_score_gemma":0.002053359,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004348455,"about_ca_topic_score_gemma":0.003003923,"domain_scores_codex":[0.9985076,0.0001775178,0.0001167278,0.0003673967,0.0006191882,0.0002114812],"domain_scores_gemma":[0.9991436,0.0001061655,0.0001025414,0.0001228749,0.0003724577,0.0001523435],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.004332832,0.0003335017,0.003187903,0.001964079,0.0003270539,0.0006836208,0.0004652311,0.004943286,0.2102646,0.005498575,0.6251039,0.1428954],"study_design_scores_gemma":[0.0007984195,0.0004340787,0.006304572,0.0004233271,0.0002229287,0.000823252,0.0002139581,0.06790686,0.157858,0.009058256,0.7554046,0.0005518022],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"methods","genre_scores_codex":[0.01933467,0.002766681,0.3156812,0.0008008132,0.001232373,0.0008182257,0.1498948,0.4898781,0.0195933],"genre_scores_gemma":[0.06029613,0.002095454,0.3651096,0.001504096,0.0003126954,0.001894832,0.5227983,0.02924454,0.01674425],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.01609235,"threshold_uncertainty_score":0.05383432,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05618134356484304,"score_gpt":0.319968135285592,"score_spread":0.263786791720749,"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."}}