{"id":"W4388668616","doi":"10.1093/nar/gkad1041","title":"PathBank 2.0—the pathway database for model organism metabolomics","year":2023,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":39,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada; Genome Alberta; Canadian Institutes of Health Research; Alberta Innovates; Genome Canada","keywords":"Metabolomics; Biology; Metabolic pathway; Database; Pathway analysis; Computational biology; Computer science; Bioinformatics; Metabolism; Genetics; Biochemistry; Gene","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":[0.002594933,0.001950179,0.001769178,0.004461784,0.001335966,0.004499398,0.003525892,0.001539491,0.0440422],"category_scores_gemma":[0.006877782,0.001781911,0.001736886,0.005736262,0.0004602408,0.005583546,0.003553939,0.003377409,0.04437452],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001117343,"about_ca_system_score_gemma":0.006568856,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003440498,"about_ca_topic_score_gemma":0.003349814,"domain_scores_codex":[0.9988802,0.0002331593,0.0001860205,0.0002578489,0.0003435918,0.00009920239],"domain_scores_gemma":[0.9976729,0.0005244058,0.0003313087,0.0006497697,0.0004438147,0.0003777303],"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":[0.001279266,0.0001074257,0.002784691,0.002549477,0.0002396819,0.0004282207,0.000174963,0.003074683,0.01068446,0.01682502,0.8924016,0.06945053],"study_design_scores_gemma":[0.0003079423,0.00009794273,0.002940503,0.0005160901,0.0001315329,0.0007363576,0.00009075912,0.006289616,0.006355289,0.0169353,0.9654731,0.0001255925],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"software","genre_scores_codex":[0.005342408,0.003978276,0.1242741,0.00234826,0.001052058,0.0005299094,0.6883246,0.1553687,0.01878171],"genre_scores_gemma":[0.01024635,0.003602708,0.1075353,0.0006125654,0.0001302319,0.0007542462,0.8617712,0.01058356,0.004763874],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.0440422,"threshold_uncertainty_score":0.1473358,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07551884971363765,"score_gpt":0.3548452200671464,"score_spread":0.2793263703535088,"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."}}