{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004954269,0.0001569171,0.0002091174,0.00002121271,0.0002284456,0.00005885003,0.001141884,0.00005683929,0.000311459],"category_scores_gemma":[0.00009103827,0.00003567223,0.00004252973,0.0004737275,0.00003794199,0.0001726318,0.0006260296,0.0001248357,0.0003302903],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003251394,"about_ca_system_score_gemma":0.00001091533,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00102034,"about_ca_topic_score_gemma":0.0009058512,"domain_scores_codex":[0.9983078,0.00009565416,0.0002703005,0.0004278102,0.0003128355,0.0005856341],"domain_scores_gemma":[0.9992961,0.0002333405,0.00004598229,0.0001943433,0.00003630506,0.000193964],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00001974149,0.00002693684,0.0005443282,0.000002844375,0.000007217598,0.00001348977,0.0002133489,0.000006823158,0.9935161,0.00004535937,0.000155555,0.005448251],"study_design_scores_gemma":[0.0002787255,0.0001764067,0.3636604,0.00006477194,0.00001447464,0.00008157666,0.0008400905,0.0001436523,0.001065552,0.000294832,0.6327688,0.0006107625],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9851767,0.0001743443,0.00002560832,0.01341869,0.00007314071,0.0003528451,0.0005459024,0.00003818857,0.0001945379],"genre_scores_gemma":[0.9974619,0.00007815606,0.0000970174,0.0002217194,0.0004947399,0.00001618606,0.0001836119,0.000001403899,0.001445273],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9924505,"threshold_uncertainty_score":0.4245324,"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."}}