{"id":"W4410317678","doi":"10.1021/acs.jproteome.4c00963","title":"ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus","year":2025,"lang":"en","type":"article","venue":"Journal of Proteome Research","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Executable; Visualization; Proteomics; Computer science; Computational biology; Biology; Data mining; Programming language; Genetics","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":[0.001482846,0.0001916808,0.0003437492,0.0004704736,0.0004053403,0.0002042243,0.0006727506,0.0001646382,0.0001892941],"category_scores_gemma":[0.00018222,0.000153278,0.00007796005,0.0009578364,0.0001902848,0.0005704741,0.0001366534,0.001045094,0.000008268959],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003496352,"about_ca_system_score_gemma":0.000703608,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004212136,"about_ca_topic_score_gemma":0.000006034224,"domain_scores_codex":[0.9976467,0.0001128198,0.0006280117,0.0003126133,0.0008104233,0.0004894208],"domain_scores_gemma":[0.997309,0.00007801062,0.0003623984,0.0005481369,0.001557123,0.0001453914],"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":[0.0007318759,0.0005886146,0.002665138,0.0005293659,0.00007511504,0.0000326945,0.000277033,0.0002996814,0.9816572,0.01003703,0.0006186947,0.002487559],"study_design_scores_gemma":[0.001233458,0.0007098456,0.0001329421,0.000726329,0.00002529669,0.0001272346,0.000554006,0.002925019,0.9670717,0.01492728,0.01129907,0.0002678435],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7021359,0.0001204905,0.2893496,0.0009038771,0.00002080791,0.002118452,0.000015001,0.0001038679,0.005231902],"genre_scores_gemma":[0.6907504,0.0001359363,0.3035727,0.00005632853,0.0002644973,0.001274372,0.000016809,0.00007350669,0.003855507],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01458552,"threshold_uncertainty_score":0.6250494,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04315564992084182,"score_gpt":0.4102176298775911,"score_spread":0.3670619799567493,"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."}}