{"id":"W2980987121","doi":"10.1093/nar/gkz916","title":"PADS Arsenal: a database of prokaryotic defense systems related genes","year":2019,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":56,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"National Development and Reform Commission; Chinese Academy of Sciences; National Natural Science Foundation of China","keywords":"Biology; Genome; Annotation; Gene; Computational biology; Function (biology); Archaea; Database; Genetics; 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":[0.001597263,0.0001474976,0.00022819,0.0001402538,0.00008346315,0.00003408654,0.0004419168,0.0002420288,0.0002060857],"category_scores_gemma":[0.0002333524,0.0001273995,0.00009257298,0.0002702541,0.0001369459,0.000007641054,0.0002981323,0.0002106137,0.0003596689],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001918274,"about_ca_system_score_gemma":0.0001442348,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006384424,"about_ca_topic_score_gemma":0.000002824755,"domain_scores_codex":[0.9977232,0.0004658581,0.0003154915,0.0004646396,0.0005721022,0.0004587241],"domain_scores_gemma":[0.9984931,0.00006107284,0.00008184966,0.0009449041,0.0002935284,0.000125564],"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":[0.0001571264,0.00006908278,0.002609199,0.000197565,0.00006436919,0.00001085781,0.00004005573,0.00002601543,0.9928208,0.001301295,0.0008619539,0.001841654],"study_design_scores_gemma":[0.0007817416,0.0009496078,0.0006455285,0.0002048525,0.00001653882,0.00005896464,0.0004254794,0.0006372109,0.969059,0.0002971079,0.02664119,0.0002827783],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9900616,0.002920507,0.0001729627,0.00007357269,0.0001945417,0.0008250999,0.00003640478,0.00001782357,0.005697515],"genre_scores_gemma":[0.9932292,0.0004909668,0.0005997487,0.00001542776,0.00009182185,0.00005958174,0.00007041679,0.0000474616,0.005395336],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02577924,"threshold_uncertainty_score":0.5195202,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03506572659863608,"score_gpt":0.3074087058478278,"score_spread":0.2723429792491917,"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."}}