{"id":"W2133464819","doi":"10.1101/gr.159384.113","title":"Comparative validation of the <i>D. melanogaster</i> modENCODE transcriptome annotation","year":2014,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":191,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Human Genome Research Institute; National Institute of Diabetes and Digestive and Kidney Diseases; National Heart, Lung, and Blood Institute; National Institute of General Medical Sciences; U.S. Public Health Service; National Institutes of Health","keywords":"Biology; Genome; Annotation; Drosophila melanogaster; Genome project; Melanogaster; Comparative genomics; Computational biology; Genomics; Drosophila pseudoobscura; Genetics; Transcriptome; Gene; Evolutionary biology; Gene expression","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":[0.0006180902,0.00007117019,0.0001110989,0.00004020459,0.0001377338,0.00001310598,0.0002494222,0.0000498115,0.00000777471],"category_scores_gemma":[0.00003518644,0.00005321975,0.00005677195,0.0001473739,0.0001509705,5.83091e-7,0.0001060757,0.00008249007,0.00000636185],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009953947,"about_ca_system_score_gemma":0.00004307116,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002419359,"about_ca_topic_score_gemma":0.00002184762,"domain_scores_codex":[0.9989697,0.0002575648,0.0001458565,0.0001911296,0.0002397969,0.000195898],"domain_scores_gemma":[0.9993547,0.00002714684,0.00004236117,0.0002952807,0.0002478971,0.00003262056],"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":[0.00002766692,0.00002181322,0.001120138,0.00001369388,0.00002851944,3.135347e-8,0.0006549748,0.001216379,0.9964086,0.0001779049,0.0001207551,0.0002095209],"study_design_scores_gemma":[0.000416692,0.0003460335,0.03370059,0.000008148208,0.00001123651,0.000002103289,0.0003759984,0.000375369,0.9340511,0.001041107,0.02955771,0.0001139449],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9944831,0.0004610323,0.00104196,0.0001804342,0.00006384165,0.0002200317,0.0000343037,8.567298e-7,0.003514502],"genre_scores_gemma":[0.9991202,0.00009872381,0.0002689789,0.00002747573,0.0001009235,0.00002310698,0.00002219691,0.000007713074,0.0003307111],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06235753,"threshold_uncertainty_score":0.2170238,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06615960783917957,"score_gpt":0.3390193304568025,"score_spread":0.2728597226176229,"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."}}