{"id":"W4385622945","doi":"10.1101/2023.08.06.552193","title":"Somrit: The Somatic Retrotransposon Insertion Toolkit","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Ontario Institute for Cancer Research","funders":"Government of Ontario; Ontario Institute for Cancer Research","keywords":"Retrotransposon; Somatic cell; Mobile genetic elements; Genome; Computational biology; Genetics; Human genome; Biology; Reference genome; Transposable element; Computer science; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002928755,0.001924676,0.001643255,0.002022526,0.0007299657,0.002199118,0.003436348,0.001328113,0.01294892],"category_scores_gemma":[0.006136265,0.001674818,0.002592615,0.001384733,0.0006992508,0.001487012,0.002783575,0.003075744,0.01937668],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005905044,"about_ca_system_score_gemma":0.001275609,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001020173,"about_ca_topic_score_gemma":0.001906377,"domain_scores_codex":[0.9977897,0.0003759701,0.0002127422,0.0005551014,0.000877712,0.0001886554],"domain_scores_gemma":[0.9981344,0.0008423409,0.0002824528,0.0003913463,0.0001985188,0.0001509086],"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":[0.004094443,0.0003483097,0.009645794,0.006502692,0.001601625,0.002309884,0.001616739,0.02036427,0.19551,0.02334102,0.4451056,0.2895596],"study_design_scores_gemma":[0.0009482951,0.0004756495,0.0102515,0.000706837,0.000430758,0.002948902,0.0002731569,0.1655415,0.2195828,0.04371048,0.5544542,0.0006759022],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.008572864,0.0006804245,0.3807032,0.0002823603,0.0003714487,0.0002821186,0.03867351,0.5656379,0.004796159],"genre_scores_gemma":[0.06418242,0.0009605068,0.6881177,0.0005744453,0.0001611314,0.00158037,0.1280846,0.1059249,0.01041391],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.01294892,"threshold_uncertainty_score":0.04331851,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02665625440174495,"score_gpt":0.2069932040216502,"score_spread":0.1803369496199053,"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."}}