{"id":"W4200139682","doi":"10.1089/phage.2021.0013","title":"Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation","year":2021,"lang":"en","type":"article","venue":"PHAGE","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":75,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"Biotechnology and Biological Sciences Research Council","keywords":"Annotation; Sequence assembly; Genome; Sequence (biology); Genome project; Genomics; Computational biology; DNA sequencing; Whole genome sequencing; Biology; World Wide Web; Information retrieval; Genetics; Computer science; Gene","routes":{"ca_aff":true,"ca_fund":false,"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":[0.000249702,0.0001090373,0.0001261425,0.00001719658,0.0001634145,0.00008444361,0.00006490079,0.00004762108,0.0009076315],"category_scores_gemma":[0.000294329,0.0001090667,0.00005231137,0.0001215463,0.00004120106,0.0004518954,0.00007330201,0.00005514054,0.0001084945],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006335551,"about_ca_system_score_gemma":0.00001201421,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0004518472,"about_ca_topic_score_gemma":0.0003680533,"domain_scores_codex":[0.9990552,0.00005159257,0.000321569,0.0003014294,0.0001014491,0.0001687398],"domain_scores_gemma":[0.9994917,0.00008567607,0.000105957,0.0001619038,0.00009457649,0.00006020596],"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":[0.00001038785,0.00004838614,0.0001882241,0.00001475379,0.000009164229,0.000004846476,0.0001579621,0.0000462239,0.9459409,0.0001730717,0.01926538,0.03414069],"study_design_scores_gemma":[0.001295591,0.00008246515,0.2642445,0.00002939929,0.00006504513,0.0000450803,0.0003092049,0.001439547,0.4809756,0.001008734,0.2500956,0.0004091877],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9699764,0.0001296961,0.02356024,0.002745633,0.0004397517,0.0002487707,0.0001241862,0.00005447906,0.002720888],"genre_scores_gemma":[0.957799,0.00006715492,0.03100097,0.001840562,0.0001679712,0.0000446926,0.0002202302,0.00001906784,0.008840383],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4649653,"threshold_uncertainty_score":0.9937929,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06642794180230718,"score_gpt":0.3861508104437872,"score_spread":0.31972286864148,"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."}}