{"id":"W2019801716","doi":"10.1093/nar/gkp667","title":"SubpathwayMiner: a software package for flexible identification of pathways","year":2009,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":215,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network","funders":"National Key Research and Development Program of China; National High-tech Research and Development Program; National Natural Science Foundation of China; National Science Foundation","keywords":"UniProt; Biology; KEGG; Computational biology; Identification (biology); Gene; Identifier; Ensembl; Bioinformatics; Computer science; Genome; Genetics; Genomics; Gene ontology; Gene expression; 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":[0.002506277,0.003359628,0.002588088,0.003657319,0.0009656989,0.002159656,0.004665603,0.001165791,0.03937596],"category_scores_gemma":[0.003944601,0.002555329,0.004097171,0.002910577,0.0006027728,0.002774836,0.002626745,0.00410725,0.02100479],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007810639,"about_ca_system_score_gemma":0.002344562,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002489439,"about_ca_topic_score_gemma":0.002578946,"domain_scores_codex":[0.9987246,0.0003322266,0.0001847522,0.0003576803,0.0002905818,0.0001100344],"domain_scores_gemma":[0.997992,0.00107366,0.0002426114,0.0003004391,0.0002771681,0.00011412],"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":[0.003213008,0.0003501053,0.006669423,0.008685722,0.00213256,0.001178239,0.001007195,0.037873,0.06060101,0.01939198,0.5574893,0.3014084],"study_design_scores_gemma":[0.001297634,0.0004240453,0.00817495,0.0005637812,0.0006718393,0.00190087,0.0002237754,0.2950449,0.08147508,0.05566389,0.5539695,0.0005897381],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.003875672,0.0005757413,0.6082128,0.0002444861,0.0001376463,0.0003762034,0.04880855,0.3351844,0.002584497],"genre_scores_gemma":[0.0272348,0.0008470798,0.8135966,0.0004181772,0.0000600703,0.002985192,0.09732239,0.05318671,0.004348964],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.03937596,"threshold_uncertainty_score":0.1317257,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03947219477116468,"score_gpt":0.3198613041370081,"score_spread":0.2803891093658435,"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."}}