{"id":"W4321443519","doi":"10.1002/cpz1.671","title":"A Guide to Gene‐Centric Analysis Using TreeSAPP","year":2023,"lang":"en","type":"article","venue":"Current Protocols","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Genome British Columbia; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Office of Science; Genome British Columbia; National Energy Research Scientific Computing Center; Joint Genome Institute; Alliance de recherche numérique du Canada; Genome Canada; U.S. Department of Energy","keywords":"Phylogenetic tree; Workflow; Computer science; Tree (set theory); Set (abstract data type); Computational biology; Protocol (science); Data mining; Documentation; Biology; Gene; Genetics; Database","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0102956,0.003003356,0.002190903,0.005300378,0.002015195,0.005445118,0.00619868,0.002420301,0.2331066],"category_scores_gemma":[0.02438209,0.005366074,0.002382072,0.004746105,0.001515443,0.004900604,0.003990826,0.008772937,0.2718009],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001593612,"about_ca_system_score_gemma":0.005266373,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003813523,"about_ca_topic_score_gemma":0.005055276,"domain_scores_codex":[0.9950847,0.001268779,0.0008951179,0.000797487,0.001538786,0.0004151234],"domain_scores_gemma":[0.9877372,0.005497527,0.000755202,0.002673071,0.002717108,0.0006198444],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0005153199,0.0001684744,0.0008731445,0.002468597,0.0001123318,0.0004991811,0.0007595719,0.001169623,0.02532552,0.01932698,0.8073401,0.1414413],"study_design_scores_gemma":[0.00009209162,0.0000654994,0.0009305156,0.0006646485,0.00002972216,0.0003570426,0.000104468,0.00189059,0.01129555,0.01590551,0.9685421,0.000122221],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.001190053,0.0016739,0.5996882,0.001012951,0.001132183,0.002299212,0.1017061,0.266923,0.02437437],"genre_scores_gemma":[0.005259947,0.002784956,0.6946629,0.002112928,0.0003577081,0.01079992,0.1156212,0.1298977,0.03850277],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.2331066,"threshold_uncertainty_score":0.7798191,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05700308403687845,"score_gpt":0.3886664617425493,"score_spread":0.3316633777056709,"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."}}