{"id":"W2979585142","doi":"10.1093/nar/gkz861","title":"PathBank: a comprehensive pathway database for model organisms","year":2019,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":149,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Canadian Institutes of Health Research; Genome Alberta; Canada Foundation for Innovation","keywords":"UniProt; Biology; DrugBank; Caenorhabditis elegans; SBML; Computational biology; KEGG; Metabolic pathway; Model organism; Systems biology; Database; Transcriptome; Genetics; World Wide Web; Markup language; Gene; Computer science","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":[0.001146569,0.00261243,0.001718627,0.005619589,0.001274287,0.003410124,0.003323758,0.001665525,0.03493621],"category_scores_gemma":[0.002410535,0.001548106,0.002541047,0.006783899,0.0004080532,0.003301858,0.002864699,0.002027435,0.02573739],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00116754,"about_ca_system_score_gemma":0.0035704,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004285102,"about_ca_topic_score_gemma":0.003534771,"domain_scores_codex":[0.9993657,0.0001014782,0.0001032707,0.0002048005,0.0001578814,0.00006688303],"domain_scores_gemma":[0.9989473,0.0003255401,0.0001599359,0.0002444877,0.0001728619,0.0001498168],"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":[0.001948484,0.0001746229,0.0029948,0.01184042,0.0005764414,0.001352122,0.0004532042,0.01863415,0.02679616,0.03494037,0.8248636,0.07542574],"study_design_scores_gemma":[0.00039438,0.0001303533,0.002964193,0.0008239638,0.0002604573,0.0009393541,0.0001507266,0.01234652,0.006755272,0.02313049,0.9519565,0.0001478074],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"software","genre_scores_codex":[0.002859331,0.002460552,0.05638513,0.0003680844,0.0001901015,0.0003014592,0.8426417,0.08639529,0.008398464],"genre_scores_gemma":[0.007652765,0.002792772,0.0549463,0.0001619934,0.00002549373,0.0006638456,0.9264997,0.004999184,0.00225787],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.03493621,"threshold_uncertainty_score":0.1168733,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0571072719321583,"score_gpt":0.3417280129624429,"score_spread":0.2846207410302846,"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."}}