{"id":"W2124514674","doi":"10.1101/gr.136184.111","title":"ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia","year":2012,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2223,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research","funders":"National Human Genome Research Institute","keywords":"ENCODE; Biology; Metadata; Chromatin immunoprecipitation; Computational biology; Computer science; Genetics; World Wide Web; Gene","routes":{"ca_aff":true,"ca_fund":false,"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":[0.04064568,0.001909719,0.002183226,0.007267593,0.002207616,0.00508754,0.008365938,0.002771485,0.01427583],"category_scores_gemma":[0.05234991,0.002836116,0.002429314,0.009338436,0.001964348,0.002172663,0.003707654,0.004839054,0.02310649],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002847782,"about_ca_system_score_gemma":0.008126065,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.009529837,"about_ca_topic_score_gemma":0.01144664,"domain_scores_codex":[0.9758195,0.01080097,0.005183729,0.002741285,0.004212795,0.001241712],"domain_scores_gemma":[0.9436358,0.0175511,0.003423954,0.01807302,0.0154223,0.001893877],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00503677,0.000540967,0.006474111,0.007076902,0.0005025991,0.001650683,0.006036328,0.005672214,0.2454122,0.05765308,0.4901712,0.1737729],"study_design_scores_gemma":[0.0002086359,0.000170669,0.004371795,0.001214592,0.0001994432,0.0006223262,0.0006379375,0.002686328,0.07110769,0.01230789,0.906259,0.0002135673],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01824954,0.005022823,0.6910421,0.005462658,0.002313622,0.00769549,0.1999028,0.03122927,0.03908172],"genre_scores_gemma":[0.009835176,0.003699615,0.7221101,0.002318658,0.000185627,0.01132143,0.2329292,0.00713951,0.01046068],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.04064568,"threshold_uncertainty_score":0.2149574,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1110899151962238,"score_gpt":0.4116946994631419,"score_spread":0.3006047842669181,"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."}}