{"id":"W4391879751","doi":"10.1021/acs.analchem.3c04501","title":"MINNO: An Open Source Software for Refining Metabolic Networks and Investigating Complex Network Activity Using Empirical Metabolomics Data","year":2024,"lang":"en","type":"article","venue":"Analytical Chemistry","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; International Microbiome Centre, University of Calgary; Government of Canada; National Institutes of Health; Alberta Innovates; Canada Foundation for Innovation","keywords":"Metabolomics; Metabolic network; Computational biology; Context (archaeology); Computer science; Genomics; Systems biology; Metabolic pathway; Identification (biology); KEGG; Biology; Bioinformatics; Genome; Ecology; Genetics; Gene; Transcriptome","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":[0.002556999,0.002670182,0.001488601,0.002448355,0.0009026414,0.00192975,0.002793635,0.001184567,0.02903666],"category_scores_gemma":[0.006013751,0.001504893,0.002528706,0.001585557,0.0005932946,0.002503811,0.002124341,0.002430725,0.005390462],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009647843,"about_ca_system_score_gemma":0.002109176,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003564446,"about_ca_topic_score_gemma":0.006616083,"domain_scores_codex":[0.9994015,0.0001025624,0.00006909076,0.0001968442,0.0001794871,0.00005052509],"domain_scores_gemma":[0.997699,0.001452354,0.0002403602,0.000283741,0.0002107503,0.0001138135],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.002746213,0.0007351699,0.02706918,0.008997753,0.003164972,0.002680918,0.002991068,0.1402175,0.09674697,0.04351717,0.2861379,0.3849951],"study_design_scores_gemma":[0.0005087977,0.0002401814,0.01024456,0.0004053045,0.0003115478,0.0008283306,0.0002348918,0.6781247,0.03920147,0.03634652,0.2332424,0.0003112209],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.02040316,0.0005914549,0.5664946,0.000331414,0.0002589611,0.000427125,0.03851779,0.3679993,0.00497626],"genre_scores_gemma":[0.0859162,0.001347773,0.7963127,0.0004678502,0.000102672,0.002436304,0.05549347,0.05178286,0.006140146],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.02903666,"threshold_uncertainty_score":0.09713733,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1251858419193357,"score_gpt":0.371309079807594,"score_spread":0.2461232378882583,"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."}}