{"id":"W4362541180","doi":"10.1158/1538-7445.am2023-2987","title":"Abstract 2987: BamQuery: a new proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens","year":2023,"lang":"en","type":"article","venue":"Cancer Research","topic":"Advanced biosensing and bioanalysis techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"","keywords":"Proteogenomics; Computational biology; Biology; Proteome; Proteomics; Exon; Genetics; RNA splicing; Intron; Genomics; RNA; Genome; Gene","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002335118,0.002594961,0.001106763,0.00147219,0.0006752837,0.00218097,0.002447209,0.001236823,0.01743453],"category_scores_gemma":[0.003528637,0.000935996,0.001261796,0.001232238,0.0006784759,0.002013431,0.002104016,0.001640078,0.007881705],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006170118,"about_ca_system_score_gemma":0.0009142578,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001610161,"about_ca_topic_score_gemma":0.001947033,"domain_scores_codex":[0.9993363,0.0001323282,0.00006951034,0.0001861473,0.0002141174,0.00006170932],"domain_scores_gemma":[0.9989079,0.0006523432,0.0001087846,0.0001069292,0.0001158037,0.0001082269],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.006150572,0.001079608,0.01263712,0.005574567,0.00108884,0.002699194,0.001912673,0.05702038,0.2490899,0.03177949,0.2846192,0.3463484],"study_design_scores_gemma":[0.001475037,0.0004855969,0.004821188,0.000399573,0.0002076072,0.001088041,0.0003121279,0.6341034,0.1202806,0.03054727,0.2058618,0.0004178059],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.02456912,0.0008084531,0.6482579,0.0006203534,0.0002015741,0.0003888193,0.02769789,0.2929388,0.004517135],"genre_scores_gemma":[0.1067316,0.001058218,0.7530785,0.0007107134,0.00009385394,0.001613585,0.06877702,0.06273584,0.005200752],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01743453,"threshold_uncertainty_score":0.05832434,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07694283564650214,"score_gpt":0.4014034146286646,"score_spread":0.3244605789821624,"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."}}