{"id":"W4417107345","doi":"10.3390/applmicrobiol5040144","title":"Composite Genome Quality Index for Pathogenic Bacterial Genomes","year":2025,"lang":"en","type":"article","venue":"Applied Microbiology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"","keywords":"Genome; Contig; Bacterial genome size; Genomics; Cluster analysis; Reference genome; Sequence assembly; Comparative genomics; Phylogenetic tree","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004041521,0.001173338,0.001205197,0.006806355,0.0006060988,0.002011034,0.001103766,0.0006111815,0.001971046],"category_scores_gemma":[0.01328018,0.0003349163,0.001510746,0.005235756,0.0004931021,0.001438599,0.002160268,0.001407461,0.0010203],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001115737,"about_ca_system_score_gemma":0.0008257087,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002323605,"about_ca_topic_score_gemma":0.002616239,"domain_scores_codex":[0.9971024,0.0004372628,0.0002837041,0.0008494065,0.001129098,0.0001980722],"domain_scores_gemma":[0.9938478,0.001725271,0.001773376,0.0005933163,0.001708653,0.0003516441],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.001805784,0.000576592,0.4881776,0.001666563,0.001357509,0.0003314128,0.0009424458,0.03780866,0.150274,0.004557994,0.01340993,0.2990915],"study_design_scores_gemma":[0.0001294879,0.001353875,0.5141808,0.0002560262,0.0004706534,0.001189045,0.0006324335,0.3766595,0.06741616,0.009331042,0.02799775,0.0003831552],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.5329223,0.002296648,0.4228004,0.0002362772,0.0001674987,0.0005831941,0.02597779,0.009124523,0.005891266],"genre_scores_gemma":[0.6088203,0.0004564068,0.3444376,0.0001164759,0.00007072372,0.0006861257,0.0435214,0.0008347863,0.001056224],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.006806355,"threshold_uncertainty_score":0.02137387,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00879455826092992,"score_gpt":0.2466111030663351,"score_spread":0.2378165448054052,"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."}}