{"id":"W2398017205","doi":"10.3835/plantgenome2015.11.0113","title":"Genome to Phenome Mapping in Apple Using Historical Data","year":2016,"lang":"en","type":"article","venue":"The Plant Genome","topic":"Horticultural and Viticultural Research","field":"Agricultural and Biological Sciences","cited_by":124,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke; Critical Systems Labs; Dalhousie University","funders":"Killam Trusts; Dalhousie University; Canada Research Chairs; U.S. Department of Agriculture; Howard Hughes Medical Institute","keywords":"Biology; Germplasm; Genome-wide association study; Single-nucleotide polymorphism; Linkage disequilibrium; Malus; Genetics; Association mapping; Phenotypic trait; Phenotype; Genome; Phenome; Domestication; Locus (genetics); Genetic association; Genotype; Horticulture; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008171363,0.0002597574,0.0003012108,0.002359059,0.000325827,0.0008227873,0.000277258,0.0002494505,0.002583606],"category_scores_gemma":[0.001805102,0.0001297437,0.0004384859,0.002280091,0.0001415504,0.0002729701,0.0005754039,0.0002203453,0.0005982373],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002625636,"about_ca_system_score_gemma":0.0002423259,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005704244,"about_ca_topic_score_gemma":0.009922192,"domain_scores_codex":[0.9995944,0.0000815397,0.00002411288,0.0002120816,0.00004990034,0.00003798927],"domain_scores_gemma":[0.9994698,0.0001955221,0.00009346337,0.00009637433,0.00007616627,0.00006876563],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003328588,0.0001421948,0.7946092,0.000356027,0.0009819302,0.001647672,0.0009483558,0.009061528,0.04356205,0.00314733,0.007387268,0.1378235],"study_design_scores_gemma":[0.00001693047,0.00003272466,0.9781985,0.00002898235,0.0001355338,0.0003071855,0.0001621929,0.005837887,0.001249055,0.001293704,0.012724,0.0000132134],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9466304,0.001551005,0.02272621,0.0002542079,0.00007464099,0.00008733584,0.02277082,0.0005342443,0.005371189],"genre_scores_gemma":[0.9472629,0.0006734626,0.02105948,0.00008936418,0.00004269232,0.00006902092,0.02912797,0.0001105435,0.001564629],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005704244,"threshold_uncertainty_score":0.01134211,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.2106003304962427,"score_gpt":0.2811539877604333,"score_spread":0.07055365726419063,"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."}}