{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002191035,0.002970753,0.0008894441,0.004080728,0.001140088,0.002963428,0.00192268,0.001137266,0.03085684],"category_scores_gemma":[0.004877047,0.001171868,0.002304606,0.003730375,0.0005879122,0.002211338,0.002637517,0.002154756,0.01996199],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007601047,"about_ca_system_score_gemma":0.001704323,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002101498,"about_ca_topic_score_gemma":0.002051256,"domain_scores_codex":[0.9990051,0.0001953265,0.0001405286,0.0003215608,0.0002563181,0.00008123286],"domain_scores_gemma":[0.9977068,0.001152489,0.0001825869,0.0003800621,0.0004585742,0.0001195087],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001801469,0.0003293669,0.006331679,0.005594326,0.000576355,0.001491164,0.0008816874,0.008550903,0.0445392,0.0233569,0.7598089,0.1467381],"study_design_scores_gemma":[0.0004442736,0.0001952801,0.01332736,0.0008552222,0.0003282877,0.001665202,0.0004687708,0.09710224,0.1006362,0.0860792,0.6985168,0.0003810015],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"methods","genre_scores_codex":[0.006186116,0.0006939326,0.3367448,0.0005826096,0.0002547588,0.0002916916,0.1686887,0.4794288,0.007128533],"genre_scores_gemma":[0.03928132,0.001136421,0.4547755,0.0007120084,0.000101964,0.001206448,0.4410705,0.05477249,0.006943487],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.03085684,"threshold_uncertainty_score":0.1032264,"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."}}