{"id":"W4415721452","doi":"10.5376/tgmb.2025.15.0023","title":"Metabolomic and Genomic Analysis of Theobromine Biosynthesis in <i>Theobroma cacao</i>","year":2025,"lang":"","type":"article","venue":"Tree Genetics and Molecular Breeding","topic":"Cocoa and Sweet Potato Agronomy","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Theobromine; Metabolomics; Theobroma; Purine; Purine metabolism; Functional genomics; Biosynthesis; Fermentation","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0006353565,0.0004692411,0.001102122,0.0004323139,0.0002045543,0.0001387176,0.0004079969,0.0002864639,0.0001233493],"category_scores_gemma":[0.00007202836,0.0002817824,0.0003758201,0.001735497,0.0003944221,0.00005498287,0.0004913945,0.0001564641,0.000001619075],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004332091,"about_ca_system_score_gemma":0.00004381019,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002197703,"about_ca_topic_score_gemma":0.002695267,"domain_scores_codex":[0.9972361,0.0001981178,0.0008394745,0.000900319,0.000235015,0.0005909232],"domain_scores_gemma":[0.9988959,0.0003052003,0.0002756197,0.0002256897,0.00009037057,0.0002072218],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00007210141,0.0001040403,0.01651894,0.0000436054,0.0008999299,0.00001167971,0.0003740155,0.0000841162,0.8790191,0.004338099,0.00002131682,0.09851301],"study_design_scores_gemma":[0.0008229786,0.0003587497,0.9288069,0.0001384116,0.003801028,0.0000054122,0.0003647614,0.01113951,0.04824712,0.001051373,0.004585954,0.0006778305],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9646458,0.03208197,0.0001205495,0.0007790732,0.0001102449,0.0003942574,0.00003958004,0.0000128994,0.001815609],"genre_scores_gemma":[0.9925157,0.006729414,0.0003672195,0.0001155034,0.00004907529,0.00001597712,0.00002062358,0.000005675957,0.0001808324],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.912288,"threshold_uncertainty_score":0.9999635,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009441084161194052,"score_gpt":0.2127266251129242,"score_spread":0.2032855409517302,"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."}}