{"id":"W4284992560","doi":"10.1101/2022.07.09.499321","title":"A Draft Human Pangenome Reference","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":74,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"U.S. National Library of Medicine; Agencia Estatal de Investigación; National Institute of Standards and Technology; Novo Nordisk Fonden; National Institute of Food and Agriculture; National Institutes of Health; Bundesministerium für Wirtschaft und Energie; Bundesministerium für Bildung und Forschung; Novo Nordisk; Heinrich-Heine-Universität Düsseldorf; German Network for Bioinformatics Infrastructure; European Commission; Oxford Nanopore Technologies; National Human Genome Research Institute; Wellcome Trust; Ministry of Education, Culture, Sports, Science and Technology; Natural Sciences and Engineering Research Council of Canada; U.S. Department of Agriculture; Howard Hughes Medical Institute; National Science Foundation","keywords":"Haplotype; Biology; Reference genome; Genetics; Computational biology; Human genome; Allele; Gene; Genome","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":[0.004626922,0.001631484,0.001489565,0.005173009,0.001485456,0.002294251,0.003063926,0.002302411,0.05498688],"category_scores_gemma":[0.01395767,0.001316916,0.001151285,0.005672925,0.0003918469,0.001480354,0.00300599,0.002040921,0.06053853],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001003321,"about_ca_system_score_gemma":0.003440624,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006048454,"about_ca_topic_score_gemma":0.005598164,"domain_scores_codex":[0.9974778,0.000552925,0.0003467886,0.0007001589,0.0007235199,0.0001988032],"domain_scores_gemma":[0.9937822,0.00122086,0.0003305418,0.001849752,0.002457204,0.0003594892],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001430047,0.0002072228,0.004204546,0.003673772,0.0002225185,0.001089204,0.0007894466,0.003220113,0.04364815,0.009483064,0.7621245,0.1699075],"study_design_scores_gemma":[0.0001594321,0.0001179888,0.00393981,0.0004447904,0.0001094581,0.0007796178,0.0001320266,0.001491555,0.012308,0.004955838,0.9754933,0.00006825435],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"dataset","genre_scores_codex":[0.01208164,0.005105367,0.1606603,0.002052754,0.001640286,0.001144169,0.7556183,0.03705953,0.02463766],"genre_scores_gemma":[0.005653898,0.0008071297,0.06781877,0.0003461002,0.00009965025,0.0006223136,0.9155347,0.003556021,0.005561374],"genre_candidate":"dataset","genre_consensus":"dataset","teacher_disagreement_score":0.05498688,"threshold_uncertainty_score":0.1839494,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01595343758177984,"score_gpt":0.2357740780113873,"score_spread":0.2198206404296074,"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."}}