{"id":"W2179324586","doi":"10.1093/nar/gkv1227","title":"Enhanced annotations and features for comparing thousands of<i>Pseudomonas</i>genomes in the Pseudomonas genome database","year":2015,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1140,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Canadian Institutes of Health Research","keywords":"Genome; Biology; Annotation; Genome project; Metadata; Comparative genomics; Computational biology; Genomics; Database; Gene; Genetics; Computer science; World Wide Web","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":[0.001224257,0.0001144921,0.0001778324,0.00009461902,0.0001560489,0.00003690376,0.0003426448,0.00007365448,0.000001848084],"category_scores_gemma":[0.0002051898,0.00008788906,0.00004364506,0.0001876835,0.0002600577,0.000001830721,0.0002665122,0.0001437906,0.000001241149],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001329168,"about_ca_system_score_gemma":0.00009292991,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000476798,"about_ca_topic_score_gemma":0.0001467671,"domain_scores_codex":[0.9987966,0.0001429353,0.0001913483,0.0003004194,0.0002430704,0.0003256041],"domain_scores_gemma":[0.9991525,0.0001124097,0.00004146938,0.0003652349,0.0002541661,0.00007426603],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0002179153,0.00008029069,0.007466952,0.00004100747,0.00004779414,0.000001643052,0.002135923,0.00009435554,0.9863342,0.0007098101,0.001437948,0.001432182],"study_design_scores_gemma":[0.01033907,0.003971118,0.3040288,0.00009204073,0.0001001817,0.00008531136,0.02668178,0.0006755963,0.4349202,0.00706093,0.2108044,0.001240579],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9902983,0.006162408,0.0003171264,0.0003024288,0.00003940928,0.0004814424,0.0001172721,0.000001604784,0.002279961],"genre_scores_gemma":[0.996361,0.0009587107,0.002122338,0.00006812523,0.0001374756,0.0001114124,0.00008442955,0.00001741394,0.0001390486],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.551414,"threshold_uncertainty_score":0.3584012,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06727502397475188,"score_gpt":0.3497283085355466,"score_spread":0.2824532845607947,"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."}}