{"id":"W4409886452","doi":"10.1093/bioinformatics/btaf269","title":"PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2","year":2025,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":39,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Alliance de recherche numérique du Canada","keywords":"Database; Computer science; Source code; Code (set theory); Process (computing); Genome; Information retrieval; Set (abstract data type); Programming language; Biology","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":[0.0002565386,0.0001311792,0.0001004071,0.00004257889,0.000233741,0.00004698346,0.000217297,0.00008035018,0.000005384798],"category_scores_gemma":[0.00008116788,0.000096957,0.00004266928,0.00009501525,0.00004165372,0.000003943195,0.0001591071,0.00005898232,0.0000131589],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001367713,"about_ca_system_score_gemma":0.0001148557,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000970889,"about_ca_topic_score_gemma":0.000113211,"domain_scores_codex":[0.9992546,0.00001633894,0.0002887,0.0001672806,0.00009443344,0.0001785955],"domain_scores_gemma":[0.9992723,0.00001672823,0.00007690743,0.0004477448,0.0001285069,0.00005785228],"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":[0.001313813,0.0004209868,0.009992079,0.0004922157,0.001031435,8.155602e-7,0.003769747,0.01690023,0.5113789,0.02390799,0.4008314,0.02996036],"study_design_scores_gemma":[0.001417252,0.0007260437,0.01574389,0.00004773344,0.0001284607,0.000006306954,0.001416888,0.01813748,0.05854353,0.000369262,0.9030539,0.0004092687],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8208442,0.0004022394,0.1708971,0.00134184,0.001523947,0.001316592,0.001705258,0.0000239395,0.001944985],"genre_scores_gemma":[0.9643146,0.0001847682,0.02849597,0.003635715,0.0003960584,0.0002234529,0.001596254,0.00001841578,0.00113477],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5022225,"threshold_uncertainty_score":0.3953792,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02756884682379836,"score_gpt":0.2633363834784288,"score_spread":0.2357675366546304,"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."}}