{"id":"W3026082741","doi":"10.1093/bioinformatics/btaa529","title":"BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways","year":2020,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":33,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; University Health Network","funders":"","keywords":"Parsing; Computer science; MIT License; License; Software; Pathway analysis; Programming language; Artificial intelligence; Biology; Operating system; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001656926,0.0001729215,0.0003077069,0.00009621701,0.00006369012,0.00003636463,0.0001693071,0.0001382336,0.00001379502],"category_scores_gemma":[0.00003115628,0.0001547834,0.0001409364,0.0003912543,0.00009365264,0.00001047991,0.0001875996,0.00007255015,0.00000755134],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008029102,"about_ca_system_score_gemma":0.00004337199,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004670031,"about_ca_topic_score_gemma":0.000004073694,"domain_scores_codex":[0.9989014,0.00001372005,0.0005687502,0.0001422552,0.0001439889,0.0002298829],"domain_scores_gemma":[0.9992208,0.00001168494,0.000265709,0.0002707496,0.00006117511,0.0001698493],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00117223,0.0006950282,0.06061093,0.003387962,0.01656375,0.00001836503,0.03559257,0.03089602,0.4073648,0.01303297,0.03760617,0.3930592],"study_design_scores_gemma":[0.002296821,0.001580547,0.008821311,0.00007299726,0.002085498,0.00002093627,0.004057637,0.8586654,0.04738319,0.0002499111,0.07336711,0.001398651],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9351509,0.001552888,0.05738457,0.000460701,0.0001543279,0.0003845676,0.0002506268,0.00003663397,0.004624833],"genre_scores_gemma":[0.9862817,0.0004820905,0.01186086,0.001008959,0.00007568151,0.000003872135,0.000257644,0.00001091527,0.00001828677],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8277694,"threshold_uncertainty_score":0.6311885,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01712591292196008,"score_gpt":0.2196263616252332,"score_spread":0.2025004487032731,"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."}}