{"id":"W2890022719","doi":"10.1093/database/bay086","title":"Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses","year":2018,"lang":"en","type":"article","venue":"Database","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"Public Health Agency of Canada","keywords":"Genome; Workflow; Computer science; Genomics; Computational biology; Comparative genomics; Identification (biology); In silico; Population; Biology; Data mining; Database; Genetics; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001282435,0.000136984,0.0001886505,0.00004511832,0.00009017598,0.00001380065,0.00009860384,0.00004773313,0.00003160177],"category_scores_gemma":[0.0000390354,0.0001162511,0.00003621844,0.00006833018,0.0002306598,0.000004464127,0.00009935968,0.0000245695,0.00000194909],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000003401672,"about_ca_system_score_gemma":0.00003876605,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002446278,"about_ca_topic_score_gemma":0.0002600477,"domain_scores_codex":[0.9992557,0.00004691714,0.0001861224,0.0003206561,0.00005446202,0.0001361367],"domain_scores_gemma":[0.9992949,0.00001865482,0.00009129717,0.0003498125,0.0001779031,0.00006740366],"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":[0.0004601674,0.00008074263,0.0009222522,0.00001651828,0.0001328036,2.413803e-7,0.0001197675,0.000002376614,0.9944093,0.00003827058,0.0033225,0.0004950076],"study_design_scores_gemma":[0.00126889,0.001565645,0.005804181,0.00002406927,0.0001791341,0.000004478855,0.0004403013,0.0006398914,0.9704586,0.00004774848,0.01935055,0.0002164557],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9796211,0.0001952187,0.001171953,0.000007344073,0.0001081807,0.0002168892,0.01852894,0.000004879262,0.0001455002],"genre_scores_gemma":[0.9715241,0.0003542704,0.01008558,0.000019869,0.0003625119,0.00002252849,0.01758562,0.0000116807,0.00003384324],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0239507,"threshold_uncertainty_score":0.4740584,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05089608623670785,"score_gpt":0.3228503856870912,"score_spread":0.2719542994503833,"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."}}