{"id":"W7116865545","doi":"10.1093/bioinformatics/btaf669","title":"RISK: a next-generation tool for biological network annotation and visualization","year":2025,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Canadian Institutes of Health Research; Canada Research Chairs","keywords":"Python (programming language); Visualization; Documentation; MIT License; Annotation; Software; Open source; License","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":[0.002955784,0.002296357,0.00123784,0.00373566,0.0009281058,0.003066297,0.003800434,0.001342919,0.07809943],"category_scores_gemma":[0.01011103,0.001422755,0.002299129,0.002360616,0.0006867563,0.004557217,0.005053015,0.003704651,0.03321946],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008462777,"about_ca_system_score_gemma":0.001961935,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002834418,"about_ca_topic_score_gemma":0.003829914,"domain_scores_codex":[0.9986305,0.0002201661,0.000130185,0.0002991433,0.0006031947,0.0001167564],"domain_scores_gemma":[0.9969391,0.001293932,0.0003681391,0.00060455,0.0004714875,0.0003228715],"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":[0.000372945,0.0001074339,0.002371421,0.001717147,0.0002902896,0.0005379674,0.0007160602,0.008870997,0.01282318,0.02440622,0.8004791,0.1473072],"study_design_scores_gemma":[0.0004717406,0.0001097712,0.004450846,0.000601574,0.0001614957,0.001425311,0.0001866448,0.1434888,0.0257657,0.1195163,0.7034345,0.0003874154],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.002190002,0.000364484,0.4292488,0.0006857186,0.0002866992,0.0001841504,0.03988175,0.522213,0.004945387],"genre_scores_gemma":[0.03639238,0.001116898,0.702861,0.001089859,0.0002322928,0.001739404,0.1298839,0.1158468,0.01083755],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.07809943,"threshold_uncertainty_score":0.2612686,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02153049484960042,"score_gpt":0.2663043655355657,"score_spread":0.2447738706859653,"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."}}