{"id":"W2126399647","doi":"10.1093/bioinformatics/btt539","title":"Pattern search in BioPAX models","year":2013,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":28,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Institute of General Medical Sciences; National Human Genome Research Institute; National Institutes of Health","keywords":"Computer science; Java; Source code; Documentation; Software; License; Data mining; Programming language","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":[0.001181273,0.001101287,0.0007761669,0.001510257,0.0007968951,0.001916803,0.001670734,0.001346405,0.007412199],"category_scores_gemma":[0.005544988,0.0005271806,0.001611538,0.002062177,0.0009532642,0.003102989,0.001986912,0.001264277,0.001700942],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009524939,"about_ca_system_score_gemma":0.0008078788,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003253996,"about_ca_topic_score_gemma":0.003930069,"domain_scores_codex":[0.9991108,0.000276454,0.0000898413,0.0002365284,0.0002283674,0.00005809288],"domain_scores_gemma":[0.9972925,0.001689637,0.0002549688,0.0004458489,0.0002230181,0.00009396163],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0006634917,0.0002433629,0.00698006,0.001079983,0.0001788743,0.001263543,0.0005321954,0.5556478,0.01153501,0.2900175,0.02433161,0.1075266],"study_design_scores_gemma":[0.00005204352,0.00004383039,0.0003013745,0.00003863252,0.00002059601,0.0002470104,0.00007226058,0.794825,0.004194241,0.1861569,0.01402892,0.00001921855],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.03967877,0.0003050357,0.9400653,0.0007458047,0.00005288683,0.0001630424,0.004927633,0.007397193,0.006664442],"genre_scores_gemma":[0.2540908,0.0005589906,0.7270516,0.0003505758,0.00004083958,0.0005603821,0.01225251,0.001176543,0.003917795],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.007412199,"threshold_uncertainty_score":0.02479625,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01528031221294748,"score_gpt":0.2275533515023761,"score_spread":0.2122730392894286,"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."}}