{"id":"W4377012855","doi":"10.1038/s41598-022-26791-x","title":"Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data","year":2023,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; University Health Network; SickKids Foundation; Microsoft (Canada); Ontario Institute for Cancer Research; Children’s Health Research Institute; Western University; University of Waterloo; Lawson Health Research Institute","funders":"Sickkids Research Institute; Natural Sciences and Engineering Research Council of Canada; Schulich School of Medicine and Dentistry, Western University; Hospital for Sick Children; Government of Canada; Ontario Institute for Cancer Research; Genome Canada; Children's Health Research Institute","keywords":"Chromatin; ChIA-PET; Computational biology; Epigenome; Epigenomics; Biology; Genomics; ChIP-sequencing; Genome; Open science; Open data; Gene; Computer science; Database; Genetics; Chromatin remodeling; Gene expression; DNA methylation; World Wide Web","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":[0.009643835,0.00220476,0.002667459,0.007794087,0.001515796,0.005031946,0.003897806,0.001573021,0.01219947],"category_scores_gemma":[0.02392606,0.001729975,0.001743635,0.007842747,0.0005856702,0.003046368,0.00436297,0.002454635,0.0126189],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001053761,"about_ca_system_score_gemma":0.004108981,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005192082,"about_ca_topic_score_gemma":0.00998662,"domain_scores_codex":[0.9942077,0.0008309645,0.0009182561,0.001981848,0.001734856,0.0003262817],"domain_scores_gemma":[0.9874433,0.003540713,0.002213424,0.003566748,0.002419797,0.0008159748],"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":[0.006637479,0.0005721733,0.05768496,0.01658805,0.00269477,0.001883635,0.001995742,0.009296943,0.199629,0.01267913,0.3842602,0.306078],"study_design_scores_gemma":[0.001069898,0.0007578341,0.06686269,0.002027791,0.001394306,0.002471186,0.0005724896,0.02371406,0.1207117,0.01386254,0.7658958,0.0006598169],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"dataset","genre_gemma":"empirical","genre_scores_codex":[0.03291976,0.004884825,0.1380375,0.0003454709,0.0004784682,0.0009092282,0.753504,0.06076046,0.008160306],"genre_scores_gemma":[0.01641583,0.0005645948,0.1390323,0.0001706655,0.00004704232,0.0007365537,0.8369615,0.004784966,0.001286527],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.01219947,"threshold_uncertainty_score":0.05100209,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1466893729848433,"score_gpt":0.3687747699494691,"score_spread":0.2220853969646258,"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."}}