{"id":"W4388682052","doi":"10.1016/j.isci.2023.108473","title":"Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results","year":2023,"lang":"en","type":"article","venue":"iScience","topic":"Genetic Associations and Epidemiology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Montreal Heart Institute","funders":"Institute of Nutrition, Metabolism and Diabetes; Government of Canada; National Institute of Diabetes and Digestive and Kidney Diseases; National Heart, Lung, and Blood Institute; Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Alliance de recherche numérique du Canada; Institut de Cardiologie de Montréal; Crohn's and Colitis Canada; Institute of Infection and Immunity; Institute of Genetics; Institut de Valorisation des Données; Fondation Institut de Cardiologie de Montréal; Zafgen; Ministère de l'Enseignement Supérieur, de la Recherche, de la Science et de la Technologie; National Institutes of Health; Canada Research Chairs; Novartis; Génome Québec; Genome British Columbia; Soy Nutrition Institute; Doris Duke Charitable Foundation; Genome Canada","keywords":"Metabolite; Annotation; Computational biology; KEGG; Metric (unit); Genetic association; Genome; Metabolomics; Computer science; Genome-wide association study; Biology; Bioinformatics; Gene; Genetics; Gene ontology; Single-nucleotide polymorphism; Genotype; Gene expression; Biochemistry","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":[0.001255049,0.0001439937,0.0002042441,0.00007413968,0.0002751355,0.00003332791,0.0001841913,0.00009138473,0.000001765694],"category_scores_gemma":[0.002706923,0.0001186673,0.00005440672,0.0005867323,0.0001308201,0.00001883435,0.00007107817,0.00007506338,0.0000394712],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006366922,"about_ca_system_score_gemma":0.0001046724,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001754926,"about_ca_topic_score_gemma":0.0001067232,"domain_scores_codex":[0.9983497,0.0001182997,0.000320606,0.0005180031,0.0003027298,0.0003906931],"domain_scores_gemma":[0.9987574,0.0002668747,0.0003072253,0.0002513092,0.0003535523,0.0000635917],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001444155,0.00007548354,0.5200388,0.00001501314,0.0003069727,0.000006203412,0.0008953436,0.009027002,0.4554928,0.0002471093,0.009878372,0.003872492],"study_design_scores_gemma":[0.0002980538,0.0001040455,0.9114249,0.000005303082,0.0000313902,0.000002590992,0.0003751669,0.0002123171,0.01805565,0.000347894,0.06894059,0.0002020836],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9913206,0.00265151,0.002623816,0.002026509,0.000320605,0.0001545321,0.0001615174,0.00004067019,0.0007002487],"genre_scores_gemma":[0.9898121,0.00264949,0.002319541,0.0005134381,0.0002492505,0.0000612988,0.0004560324,0.000010939,0.003927913],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4374371,"threshold_uncertainty_score":0.483911,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02093917129537697,"score_gpt":0.296596566580715,"score_spread":0.2756573952853381,"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."}}