{"id":"W2990822156","doi":"10.3389/fgene.2019.01192","title":"LD-annot: A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes","year":2019,"lang":"en","type":"article","venue":"Frontiers in Genetics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph; Centre hospitalier universitaire de Québec; Université Laval","funders":"Natural Resources Canada; Genome British Columbia; Canadian Food Inspection Agency; Genome Canada","keywords":"Single-nucleotide polymorphism; Gene; Genetics; Biology; Computational biology; Computer science; Candidate gene; Bioinformatics; Genotype","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002022633,0.0003245241,0.000372984,0.0001497254,0.0001079012,0.00006966272,0.0003788702,0.0001875335,0.000005419753],"category_scores_gemma":[0.00007503025,0.0002956635,0.00009704433,0.0002303796,0.0001022054,0.000002643597,0.0001709705,0.00009003466,0.00001615433],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004038528,"about_ca_system_score_gemma":0.0002642346,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006052067,"about_ca_topic_score_gemma":0.00006297635,"domain_scores_codex":[0.9981406,0.00003266268,0.0005474641,0.0004907086,0.0002113234,0.0005772163],"domain_scores_gemma":[0.9988467,0.00002522035,0.000122543,0.0006229596,0.0002288177,0.0001537991],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00175276,0.0005115501,0.3861778,0.0008443624,0.001235756,0.000011437,0.003403045,0.08475607,0.3441145,0.0005374267,0.02652484,0.1501305],"study_design_scores_gemma":[0.0110417,0.009671489,0.1734487,0.0002508419,0.0004715132,0.00005018986,0.003078439,0.1427183,0.08569422,0.002177182,0.5672546,0.004142902],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.905292,0.001174587,0.09013911,0.0003126459,0.0004918078,0.002022585,0.0001647599,0.00001275035,0.0003896947],"genre_scores_gemma":[0.3689903,0.000411118,0.6285037,0.0008631701,0.0001625928,0.0003253482,0.0001173755,0.00006833434,0.0005580559],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.5407298,"threshold_uncertainty_score":0.9999496,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005746505884505743,"score_gpt":0.2235873805613639,"score_spread":0.2178408746768582,"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."}}