{"id":"W2558585189","doi":"10.1093/nar/gkw1082","title":"pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis","year":2016,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":119,"is_retracted":false,"has_abstract":true,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network; University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada; U.S. Department of Defense","keywords":"Biology; Unavailability; Computational biology; Proteome; Gene; Biological pathway; Pathway analysis; Human proteome project; Genetics; Proteomics; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001254364,0.0001539409,0.0002113602,0.0001873358,0.0004737213,0.00009922144,0.0002159716,0.000258161,0.00002098763],"category_scores_gemma":[0.0001219965,0.0001162497,0.00007705384,0.0003012953,0.0002142337,0.00001307105,0.0002514962,0.0001351646,0.000002414634],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004372323,"about_ca_system_score_gemma":0.00007172403,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002060295,"about_ca_topic_score_gemma":0.00006648131,"domain_scores_codex":[0.9983275,0.0001693627,0.0003028551,0.000436872,0.000270306,0.000493093],"domain_scores_gemma":[0.9988697,0.00007279737,0.00008757201,0.0004473033,0.0002853632,0.0002372686],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001552045,0.0001761312,0.01746877,0.00003384404,0.0007941328,0.000003598444,0.0007684976,0.00001623922,0.8932745,0.00114916,0.004715845,0.08144408],"study_design_scores_gemma":[0.009896399,0.007292725,0.2325496,0.0000950508,0.000507978,0.00003145895,0.001606078,0.01287795,0.1534138,0.005197003,0.5746307,0.00190128],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9941453,0.0004218344,0.003139573,0.000300678,0.00002187741,0.000467232,0.0006057509,0.0000216075,0.0008761867],"genre_scores_gemma":[0.996206,0.0001870224,0.001020683,0.00007775459,0.0002073077,0.00007462013,0.000649057,0.00002628383,0.001551216],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7398607,"threshold_uncertainty_score":0.4740523,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02667941898478075,"score_gpt":0.3102537604734462,"score_spread":0.2835743414886654,"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."}}