{"id":"W2998008364","doi":"10.1093/nar/gkz989","title":"pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species","year":2019,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":77,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Toronto Western Hospital; University Health Network; Memorial University of Newfoundland","funders":"Natural Sciences and Engineering Research Council of Canada; Atlantic Canada Opportunities Agency; Canada Foundation for Innovation; Ontario Research Foundation; International Business Machines Corporation","keywords":"Biology; Domestication; Resource (disambiguation); Evolutionary biology; Computational biology; Genetics; Ecology","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":[0.0007022143,0.0001282558,0.0001820936,0.000156746,0.0002835423,0.0001176965,0.0001868175,0.0001585928,0.00003156668],"category_scores_gemma":[0.00004004918,0.000115198,0.00005051988,0.0002567358,0.0001768196,0.000009739003,0.0002206579,0.0001492622,0.000004789552],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001868497,"about_ca_system_score_gemma":0.00005433596,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000008353076,"about_ca_topic_score_gemma":0.00002106784,"domain_scores_codex":[0.998773,0.00006430451,0.0002170147,0.0003760869,0.0002113906,0.0003581728],"domain_scores_gemma":[0.9991238,0.00003856443,0.00004767257,0.0004382654,0.0001926252,0.0001591002],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0001826616,0.0001780626,0.003523368,0.000091966,0.0004400712,0.000001786862,0.001402392,0.001441099,0.9673769,0.01337197,0.002267353,0.009722338],"study_design_scores_gemma":[0.006462411,0.005736924,0.07057845,0.00005056529,0.0004790749,0.0000293632,0.007635181,0.7506177,0.0493868,0.03061744,0.07663435,0.001771716],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9864417,0.0002383365,0.01076398,0.0001707785,0.00001286673,0.0004857313,0.00008359955,0.00001216573,0.001790815],"genre_scores_gemma":[0.9923724,0.00009507288,0.003998306,0.0001035389,0.00006298204,0.00003408494,0.0003801985,0.00002173652,0.002931681],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9179901,"threshold_uncertainty_score":0.469764,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03107491543850105,"score_gpt":0.3192241642857758,"score_spread":0.2881492488472747,"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."}}