{"id":"W2188035077","doi":"10.1093/nar/gkv1203","title":"ORegAnno 3.0: a community-driven resource for curated regulatory annotation","year":2015,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":235,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; University of British Columbia; Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency","funders":"National Cancer Institute; National Human Genome Research Institute; National Institute of Mental Health","keywords":"Annotation; Biology; Resource (disambiguation); Computational biology; Regulatory sequence; Database; Information retrieval; Transcription factor; Gene; Bioinformatics; Computer science; Genetics","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001543407,0.0001172356,0.0001230193,0.00009453871,0.0003495148,0.00006652174,0.000470327,0.0002018864,0.000007048852],"category_scores_gemma":[0.0004715581,0.0001184305,0.00005928568,0.0002013444,0.0002052513,0.000005467899,0.0002871249,0.0003345996,0.00002747282],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008212572,"about_ca_system_score_gemma":0.0002413544,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004077321,"about_ca_topic_score_gemma":0.00004963532,"domain_scores_codex":[0.9984671,0.0003994341,0.000193197,0.0002425514,0.000311192,0.0003864566],"domain_scores_gemma":[0.998409,0.00005260651,0.00005261774,0.0006607056,0.0006476639,0.0001774027],"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":[0.0007662186,0.0003104101,0.002907905,0.0001126565,0.0001176627,0.000004437249,0.002102509,0.001160932,0.8332515,0.00192618,0.1492946,0.008044986],"study_design_scores_gemma":[0.005269505,0.003743736,0.009464378,0.00007115128,0.00002908628,0.0000279011,0.0094226,0.03431519,0.0772413,0.005578704,0.8540186,0.0008177978],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9938927,0.0001356929,0.0007740344,0.0003249102,0.00005140753,0.0003875491,0.00004588974,0.00002090737,0.004366894],"genre_scores_gemma":[0.994476,0.00001646331,0.002471653,0.0001038815,0.0001824948,0.00005907597,0.000640036,0.00004676655,0.002003695],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7560102,"threshold_uncertainty_score":0.4829455,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06683767200651129,"score_gpt":0.3455675173957038,"score_spread":0.2787298453891925,"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."}}