{"id":"W2316956853","doi":"10.1016/j.meegid.2014.01.003","title":"Metadata beyond the sequence enables the phylodynamic inference of bovine viral diarrhea virus type 1a isolates from Western Canada","year":2014,"lang":"en","type":"article","venue":"Infection Genetics and Evolution","topic":"Animal Disease Management and Epidemiology","field":"Agricultural and Biological Sciences","cited_by":27,"is_retracted":false,"has_abstract":false,"ca_institutions":"Shared Health; University of Saskatchewan; University of Calgary","funders":"","keywords":"Viral phylodynamics; Phylogenetic tree; Biology; Clade; Most recent common ancestor; Evolutionary biology; Population; Phylogeography; Phylogenetics; Sequence (biology); Genetics; Computational biology; Demography; Gene","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"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":[0.001142016,0.0002712503,0.0004546099,0.003921769,0.002453729,0.002473492,0.0009268973,0.0004266193,0.003114782],"category_scores_gemma":[0.008835195,0.0003894325,0.000402299,0.005946808,0.0005267956,0.0009731107,0.001210983,0.000726918,0.0007363643],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.008195201,"about_ca_system_score_gemma":0.02521104,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.9593421,"about_ca_topic_score_gemma":0.9714959,"domain_scores_codex":[0.9992056,0.0000969807,0.00006319363,0.0002275551,0.0002489218,0.0001576493],"domain_scores_gemma":[0.9956325,0.000940723,0.000485182,0.0006193124,0.001911063,0.0004113049],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0007044484,0.0001149555,0.7259587,0.0004641208,0.0002620523,0.0005385302,0.004792746,0.02096009,0.02884104,0.01409227,0.02990527,0.1733658],"study_design_scores_gemma":[0.00006377098,0.00007328936,0.7209646,0.0007079947,0.0002436599,0.0004432726,0.004799987,0.06147578,0.01345342,0.01202144,0.1855743,0.0001785884],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7260221,0.001415497,0.04372179,0.001685112,0.0001155496,0.0002260246,0.2021105,0.002470632,0.02223275],"genre_scores_gemma":[0.8585743,0.0009328391,0.04934445,0.0003476247,0.00004009656,0.00009167234,0.08424299,0.0004557007,0.005970207],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04065794,"threshold_uncertainty_score":0.08179468,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01994087323395188,"score_gpt":0.2281632120697825,"score_spread":0.2082223388358306,"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."}}