{"id":"W4368358104","doi":"10.1093/nar/gkad326","title":"Proksee: in-depth characterization and visualization of bacterial genomes","year":2023,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1720,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; Public Health Agency of Canada; University of Alberta","funders":"Alliance de recherche numérique du Canada; Genome Alberta; Genome Canada","keywords":"JSON; GenBank; Visualization; Computer science; Graphical user interface; Web server; Reference genome; Biology; Contig; Genome; File format; Information retrieval; Data mining; Database; The Internet; World Wide Web; Operating system; Genetics","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":[0.0008144085,0.001194282,0.001023449,0.00269497,0.0007229944,0.002277777,0.001432089,0.0007828231,0.03906389],"category_scores_gemma":[0.002109352,0.0006775261,0.0009670933,0.001805918,0.0002173943,0.002142947,0.002658853,0.001732842,0.01686183],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003493655,"about_ca_system_score_gemma":0.0008979564,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001528511,"about_ca_topic_score_gemma":0.002513204,"domain_scores_codex":[0.9995525,0.00007239175,0.00003844008,0.0001125526,0.0001590583,0.00006487392],"domain_scores_gemma":[0.9993444,0.0001955175,0.00008493757,0.0001267507,0.0001242246,0.0001240574],"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":[0.001781869,0.0001374412,0.005581323,0.005644379,0.0003204244,0.001087005,0.002618161,0.003073945,0.2741413,0.009858321,0.4839637,0.2117921],"study_design_scores_gemma":[0.000354327,0.0002102351,0.01870742,0.0006800642,0.0001375829,0.002400468,0.001116673,0.04442571,0.1177618,0.01262453,0.8011507,0.0004304744],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.06010521,0.002725351,0.3572237,0.001602839,0.0005240244,0.000543976,0.2627886,0.2868818,0.02760439],"genre_scores_gemma":[0.1514562,0.003103151,0.5465322,0.0004950507,0.000156274,0.0007160812,0.2394103,0.04388748,0.01424337],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.03906389,"threshold_uncertainty_score":0.1306818,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03928388929651389,"score_gpt":0.336911381044976,"score_spread":0.2976274917484621,"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."}}