{"id":"W4403393007","doi":"10.1099/mgen.0.001293","title":"The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary; AIDS Vancouver; Mila - Quebec Artificial Intelligence Institute; Genome Canada; Michael Smith Health Research BC; Sunnybrook Health Science Centre; BC Centre for Disease Control; Women and Children’s Health Research Institute; Ontario Genomics; University of Alberta; Indoc Research; Université de Montréal; McGill Genome Centre; University of Toronto; Western University; McGill University; Simon Fraser University; Public Health Agency of Canada; Ontario Institute for Cancer Research; University of British Columbia; Montreal Heart Institute","funders":"National Cancer Institute; Canadian Institutes of Health Research; Institut de Valorisation des Données; Fonds de Recherche du Québec - Santé; Michael Smith Health Research BC; Alliance de recherche numérique du Canada; Genome Alberta; Public Health Agency of Canada; Simon Fraser University; Government of Ontario; Genome Canada; National Institutes of Health; Ontario Genomics; Government of Canada; Public Health Agency; Innovation, Science and Economic Development Canada; Canarie","keywords":"Data sharing; Pandemic; Interoperability; Big data; Suite; Genomics; Data access; Computer science; Data science; World Wide Web; Genome; Coronavirus disease 2019 (COVID-19); Database; Biology; Political science; Medicine; Data mining; Genetics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001881038,0.0002102339,0.0003958757,0.0001404186,0.0005548681,0.000467235,0.0008005125,0.0001830725,0.000003523109],"category_scores_gemma":[0.0003131353,0.0001558789,0.00005618517,0.0001116177,0.000594688,0.0001468792,0.0007365613,0.0003170174,0.00002330475],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002356608,"about_ca_system_score_gemma":0.001372137,"about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_topic_score_codex":0.09380674,"about_ca_topic_score_gemma":0.35941,"domain_scores_codex":[0.9980897,0.00009806503,0.0003934262,0.0007076785,0.00007028758,0.0006408545],"domain_scores_gemma":[0.9986771,0.0005124948,0.00005927682,0.0006127486,0.00004571043,0.00009269245],"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":[0.0004705016,0.00001568348,0.004500445,0.0001420981,0.0002692686,0.000179991,0.0008356962,3.422986e-7,0.9345372,0.00178649,0.0406229,0.01663933],"study_design_scores_gemma":[0.0005753224,0.0001596259,0.0008898463,0.00003864938,0.00008671636,0.0004300685,0.0001710843,0.001177589,0.0147872,0.001189897,0.9803008,0.0001931837],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9822983,0.01008963,0.00002482436,0.004367827,0.0002162986,0.001086168,0.0004480372,0.00002932792,0.001439591],"genre_scores_gemma":[0.9338441,0.0004342679,0.001874914,0.06208411,0.001084019,0.00007165763,0.0001407434,0.000104516,0.0003617147],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9396779,"threshold_uncertainty_score":0.9122277,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1304469555089388,"score_gpt":0.3958323842994825,"score_spread":0.2653854287905437,"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."}}