{"id":"W4396940192","doi":"10.1093/bib/bbae229","title":"AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods","year":2024,"lang":"en","type":"article","venue":"Briefings in Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":20,"is_retracted":false,"has_abstract":true,"ca_institutions":"Wilfrid Laurier University; University of Waterloo","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Genome; Visualization; Upload; Genome browser; Interactive visualization; Computational biology; Bacterial genome size; Gene Annotation; Annotation; Biology; KEGG; Computer science; Gene; Genomics; Data mining; Genetics; World Wide Web; Gene ontology","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":[0.002265281,0.001704426,0.001832189,0.003826346,0.001092468,0.003131437,0.002673314,0.0009931689,0.01887426],"category_scores_gemma":[0.003926313,0.001284635,0.001736733,0.002442155,0.0005266754,0.003556697,0.003651193,0.002562599,0.01010921],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005658253,"about_ca_system_score_gemma":0.001255845,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00245423,"about_ca_topic_score_gemma":0.004074723,"domain_scores_codex":[0.9988968,0.0001898817,0.00009664609,0.0002619737,0.0004468269,0.0001078512],"domain_scores_gemma":[0.9981095,0.000759315,0.0001382561,0.0003171398,0.0003150306,0.0003607995],"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":[0.003321122,0.0006042156,0.01874182,0.002792106,0.0007093126,0.001588938,0.00224626,0.008366133,0.1774355,0.01933411,0.4599674,0.3048931],"study_design_scores_gemma":[0.0005585951,0.0003190691,0.01846487,0.0005566142,0.0002181477,0.001651683,0.0009166577,0.1451469,0.1331639,0.03048366,0.6679636,0.0005561802],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.03946552,0.002124196,0.4552135,0.001093088,0.0005067656,0.000445453,0.08823281,0.3998559,0.01306279],"genre_scores_gemma":[0.1074212,0.002987292,0.6699541,0.0006610039,0.0002211978,0.001344399,0.1626601,0.04456236,0.01018846],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01887426,"threshold_uncertainty_score":0.06314069,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00832843084101445,"score_gpt":0.2627670856006795,"score_spread":0.2544386547596651,"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."}}