{"id":"W4388410058","doi":"10.1093/nar/gkad964","title":"IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata","year":2023,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":89,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Nuclear Security Administration; Office of Science; Medical Research Council; Joint Genome Institute; U.S. Department of Energy","keywords":"Plasmid; Biology; Metadata; Horizontal gene transfer; Genome; Database; Genetics; Mobile genetic elements; Gene; Computational biology; World Wide Web; Computer science","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":[],"consensus_categories":[],"category_scores_codex":[0.0004563733,0.0001214849,0.0001869655,0.0001409438,0.0001878482,0.00005148651,0.0001954049,0.00006176206,0.00001920762],"category_scores_gemma":[0.00009442845,0.00009873686,0.00002186938,0.0003109149,0.0004016627,0.000003506013,0.0006151526,0.0001068663,0.000005249282],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005279167,"about_ca_system_score_gemma":0.00007080997,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001599853,"about_ca_topic_score_gemma":0.0001435667,"domain_scores_codex":[0.9988203,0.00008973773,0.0001518977,0.000412999,0.0002376877,0.0002873593],"domain_scores_gemma":[0.999186,0.0001092633,0.00003541452,0.0004152238,0.0001566431,0.00009744382],"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":[0.0001158788,0.00003383297,0.04259758,0.00004916272,0.0004109638,0.000008891359,0.0004865227,0.00001158529,0.9509346,0.0003433352,0.001240705,0.003766955],"study_design_scores_gemma":[0.00355094,0.002090588,0.5481228,0.00006678377,0.0002747089,0.00003038933,0.008347612,0.0007568804,0.2600348,0.001955031,0.1738572,0.0009123177],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9910272,0.006942767,0.00004060996,0.0002597068,0.00001847622,0.0001954345,0.001104288,0.000003830216,0.0004077331],"genre_scores_gemma":[0.9877834,0.008450832,0.002781316,0.00002602194,0.00006007362,0.00003337236,0.0002980926,0.00002323218,0.0005436955],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6908998,"threshold_uncertainty_score":0.4026372,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05222245131801095,"score_gpt":0.3254994627776809,"score_spread":0.27327701145967,"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."}}