{"id":"W4309305948","doi":"10.1093/nar/gkac1049","title":"MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters","year":2022,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Microbial Natural Products and Biosynthesis","field":"Medicine","cited_by":453,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa; Simon Fraser University; University of Manitoba","funders":"National Center for Complementary and Integrative Health; National Institute of Allergy and Infectious Diseases; Fundação para a Ciência e a Tecnologia; Danmarks Grundforskningsfond; Biotechnology and Biological Sciences Research Council; Directorate for Biological Sciences; National Institutes of Health; Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro; National Research Foundation of Korea; Cooperative Research Centres, Australian Government Department of Industry; University of Strathclyde; U.S. Department of Energy; European Commission; Deutsche Forschungsgemeinschaft; National Research Foundation; National Science Foundation; UK Research and Innovation; Government of the United Kingdom; Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional; Novo Nordisk Fonden; Netherlands eScience Center; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Consejo Nacional de Ciencia y Tecnología; National Institute of General Medical Sciences; Novo Nordisk","keywords":"Biology; Gene; Computational biology; Genetics","routes":{"ca_aff":true,"ca_fund":false,"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":["sts","insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.002256198,0.0002295925,0.0003905127,0.000592878,0.001347271,0.00008444532,0.0007590318,0.00008957466,0.002814549],"category_scores_gemma":[0.0002650657,0.0001976236,0.0001379711,0.001346389,0.0002613985,0.00007412134,0.001655657,0.001722418,0.0004120324],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005509994,"about_ca_system_score_gemma":0.0001775518,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006005828,"about_ca_topic_score_gemma":0.00001629182,"domain_scores_codex":[0.9961456,0.000961573,0.0003598826,0.0005091865,0.001183184,0.0008405954],"domain_scores_gemma":[0.9980799,0.0001439777,0.00004886078,0.001044227,0.0002798283,0.0004032345],"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":[0.0009278517,0.0005225008,0.0003038893,0.00006044301,0.00009098244,0.00009818924,0.002359241,0.00001788658,0.9665638,0.00001902315,0.02476666,0.004269515],"study_design_scores_gemma":[0.00136568,0.002413918,0.00163124,0.00008286744,0.00004182425,0.0002673322,0.004261816,0.0002506635,0.8462201,0.0000288741,0.1430808,0.0003549364],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9850652,0.0001465745,0.000005363732,0.01043201,0.0001849052,0.001270971,0.00009311279,0.0001199325,0.002681945],"genre_scores_gemma":[0.992744,0.00003013071,0.001567648,0.001693605,0.0001380822,0.00003232064,0.000120113,0.00007288639,0.003601253],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1203437,"threshold_uncertainty_score":0.9999529,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07228368222249668,"score_gpt":0.3564222768261625,"score_spread":0.2841385946036658,"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."}}