{"id":"W4409340383","doi":"10.1038/s42255-025-01283-0","title":"Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics","year":2025,"lang":"en","type":"article","venue":"Nature Metabolism","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":65,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of British Columbia","funders":"National Cancer Institute; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Canada Research Chairs; U.S. Department of Health and Human Services","keywords":"Metabolomics; Computational biology; Pathway analysis; Gene; Biology; Genetics; Chemistry; Bioinformatics; Gene expression","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":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.00516201,0.001268366,0.002028132,0.002202137,0.001273258,0.003925578,0.001876652,0.001696207,0.002276941],"category_scores_gemma":[0.01382729,0.0007886776,0.00104663,0.002650922,0.005884429,0.006790749,0.003510883,0.005388382,0.00202941],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005146958,"about_ca_system_score_gemma":0.001496469,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008671989,"about_ca_topic_score_gemma":0.001165589,"domain_scores_codex":[0.9967543,0.001411351,0.0002253614,0.0007051392,0.0007769176,0.0001268658],"domain_scores_gemma":[0.9895956,0.003661797,0.000706972,0.004400576,0.001163689,0.000471432],"domain_codex":null,"domain_gemma":"methods","domain_candidate":"methods","domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.001567318,0.0003868905,0.01785685,0.002153213,0.0006368461,0.001681464,0.001033114,0.002309205,0.2508999,0.2989243,0.01978715,0.4027638],"study_design_scores_gemma":[0.0001082442,0.0004014736,0.01376007,0.0003922704,0.0003216537,0.003279018,0.0004765776,0.01061574,0.09333026,0.7084473,0.1686672,0.0002001331],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03920867,0.0121677,0.9079915,0.01504756,0.00218667,0.0001161818,0.002126795,0.003939806,0.01721502],"genre_scores_gemma":[0.3107091,0.01213951,0.6560254,0.0104385,0.001510214,0.0002446374,0.001048806,0.001800481,0.006083427],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.994838,"threshold_uncertainty_score":0.0272997,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007464418621644259,"score_gpt":0.2659751045875354,"score_spread":0.2585106859658912,"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."}}