{"id":"W3107629351","doi":"10.1038/s41467-020-19986-1","title":"Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences","year":2020,"lang":"en","type":"article","venue":"Nature Communications","topic":"Microbial Natural Products and Biosynthesis","field":"Medicine","cited_by":382,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University; Hamilton Health Sciences; Canada's Michael Smith Genome Sciences Centre; Michael Smith Health Research BC","funders":"Canadian Institutes of Health Research; Canada Research Chairs; Joint Programming Initiative on Antimicrobial Resistance","keywords":"Metagenomics; Computational biology; Genome; Prism; Biology; Secondary metabolite; Antibiotics; Antibiotic resistance; Genomics; Genetics; Gene","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":[0.00004552164,0.0001240893,0.000314557,0.00003816469,0.0001153328,0.00001309326,0.0002724649,0.0003223174,0.00009310308],"category_scores_gemma":[0.0001502397,0.0000885776,0.0000646824,0.0002021355,0.000310666,0.00007985242,0.0002402124,0.0009983772,0.00000171451],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001526792,"about_ca_system_score_gemma":0.00005532999,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005178311,"about_ca_topic_score_gemma":0.00001449803,"domain_scores_codex":[0.9992592,0.0001372564,0.0001832909,0.0002419932,0.00008125712,0.00009704189],"domain_scores_gemma":[0.9989533,0.0001436478,0.0001150048,0.0005233283,0.0001775943,0.00008705324],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0001082289,0.00003603051,0.001753859,0.00002979461,0.000103051,7.287024e-7,0.0002408286,2.583582e-7,0.9942563,0.0001151466,0.0003427636,0.003012987],"study_design_scores_gemma":[0.00068454,0.0001626861,0.5776623,0.00003155785,0.0002112815,0.00002565632,0.0001215204,0.0000751094,0.3067656,0.0001452621,0.1139644,0.0001500909],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9591828,0.02129825,0.000006454804,0.01618929,0.00007180735,0.0002895041,0.002819464,0.00004370477,0.00009870294],"genre_scores_gemma":[0.989598,0.002219652,0.00582457,0.001561149,0.000168551,6.370333e-7,0.0006138942,0.000007224045,0.00000626965],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6874908,"threshold_uncertainty_score":0.4337508,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04359839612373137,"score_gpt":0.2762836905992667,"score_spread":0.2326852944755353,"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."}}