{"id":"W3131765257","doi":"10.1038/s41589-020-00724-z","title":"A community resource for paired genomic and metabolomic data mining","year":2021,"lang":"en","type":"article","venue":"Nature Chemical Biology","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":129,"is_retracted":false,"has_abstract":true,"ca_institutions":"Memorial University of Newfoundland","funders":"Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie – Hans-Knöll-Institut; Carl R. Woese Institute for Genomic Biology; National Center for Complementary and Integrative Health; National Institute of General Medical Sciences; National Cancer Institute; Harvard University; Det Sundhedsvidenskabelige Fakultet, Københavns Universitet; School of Chemistry, University of Nottingham; Consejo Superior de Investigaciones Científicas; Fundação para a Ciência e a Tecnologia; Leibniz-Gemeinschaft; Great Lakes Bioenergy Research Center; Universität Potsdam; Directorate for Biological Sciences; Novo Nordisk Foundation Center for Basic Metabolic Research; Novo Nordisk Fonden; Wageningen University and Research; Faculty of Health and Medical Sciences, University of Western Australia; University of Illinois at Urbana-Champaign; Rheinische Friedrich-Wilhelms-Universität Bonn; Princeton University; Universiteit Antwerpen; Northwestern University; Universidade do Porto; Universidade de São Paulo; Wageningen University Fund; Sungkyunkwan University; Jenderal Soedirman University; Technische Universität Berlin; Sunchon National University; University of California, San Diego; Memorial University of Newfoundland; University of Wisconsin-Madison; U.S. Department of Energy; Yale University; Eberhard Karls Universität Tübingen; University of Glasgow; Netherlands eScience Center; Sookmyung Women's University; European Commission; Instituut voor Tropische Geneeskunde; Skaggs School of Pharmacy and Pharmaceutical Sciences; Helsingin Yliopisto; Deutsches Zentrum für Infektionsforschung; Novo Nordisk; Georgia Institute of Technology; National Research Centre; Universidad de Málaga; University of California Merced; National Institutes of Health; Biotechnology and Biological Sciences Research Council; Purdue University; National Science Foundation","keywords":"Metabolomics; Metabolome; Identification (biology); Genomics; Computational biology; Metabolite; Biology; Omics; Data science; Genome; Computer science; Bioinformatics; Genetics; Gene; Ecology; 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":[0.0004036272,0.0001741965,0.0003200682,0.00002802435,0.0001423161,0.00001591533,0.0004348499,0.0005464138,0.000008098097],"category_scores_gemma":[0.001300249,0.0001565649,0.00006872202,0.00008227789,0.0001704838,0.000002317309,0.001235702,0.0004045856,7.331085e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008901804,"about_ca_system_score_gemma":0.00005204062,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004502316,"about_ca_topic_score_gemma":0.00001944889,"domain_scores_codex":[0.9988087,0.0001438554,0.0001939908,0.0005281843,0.00003683234,0.0002884206],"domain_scores_gemma":[0.9988393,0.0001333878,0.00007266521,0.0008020225,0.00007959417,0.00007302496],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001071564,0.00004089374,0.0006890065,0.00002050206,0.0001645027,8.427713e-7,0.00001979346,6.659903e-8,0.9864206,0.0005407388,0.008626919,0.003369021],"study_design_scores_gemma":[0.0007361754,0.00007803949,0.000774575,0.000003764982,0.00006605018,0.00003286056,0.0001490784,0.00002389493,0.5043988,0.0005791226,0.4929608,0.0001968466],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9708201,0.02673247,0.0002654706,0.001019109,0.0001395905,0.0001270715,0.0004031233,0.00001446317,0.0004785393],"genre_scores_gemma":[0.9793045,0.0008236183,0.01399768,0.001517236,0.0003608062,0.00002029364,0.003750133,0.00002187349,0.0002038506],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4843338,"threshold_uncertainty_score":0.6384532,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03108061247956096,"score_gpt":0.3038772829792303,"score_spread":0.2727966704996694,"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."}}