{"id":"W2107949418","doi":"10.1186/gb-2014-15-3-r53","title":"An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge","year":2014,"lang":"en","type":"article","venue":"Genome biology","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":432,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; SickKids Foundation; University of Toronto; Hospital for Sick Children; McGill University and Génome Québec Innovation Centre; Alberta Children's Hospital; University of Calgary; McGill University; Children's Hospital of Eastern Ontario; University of Ottawa","funders":"National Institute of General Medical Sciences; National Heart, Lung, and Blood Institute; National Human Genome Research Institute; Eunice Kennedy Shriver National Institute of Child Health and Human Development; Manton Center for Orphan Disease Research, Boston Children's Hospital; Howard Hughes Medical Institute","keywords":"Biology; CLARITY; Human genetics; Genome Biology; Personal genomics; Computational biology; Best practice; Interpretation (philosophy); Genome; DNA sequencing; Data science; Evolutionary biology; Whole genome sequencing; Genomics; Genetics; DNA; Gene; Computer science; Political science","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":["metaresearch"],"consensus_categories":["metaresearch"],"category_scores_codex":[0.6877689,0.002414873,0.003407661,0.01363911,0.009857905,0.03410097,0.0182798,0.01773454,0.004610557],"category_scores_gemma":[0.5631242,0.002905699,0.00437368,0.01048882,0.02615946,0.02141785,0.03603841,0.03731759,0.003689314],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.02116806,"about_ca_system_score_gemma":0.1473901,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01219026,"about_ca_topic_score_gemma":0.006098785,"domain_scores_codex":[0.4025034,0.365716,0.07516292,0.02911566,0.1144013,0.01310071],"domain_scores_gemma":[0.1589875,0.3407709,0.04818588,0.1414821,0.2731501,0.03742364],"domain_codex":null,"domain_gemma":"reporting","domain_candidate":"reporting","domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0003992126,0.001275482,0.01741782,0.004029128,0.0003705245,0.001501145,0.0785209,0.005187829,0.01024578,0.2265389,0.1405717,0.5139416],"study_design_scores_gemma":[0.0001536659,0.0008408481,0.02322298,0.01513939,0.0002061154,0.0023325,0.0325747,0.0132992,0.008034282,0.1580085,0.7454207,0.000767166],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01748568,0.009363759,0.6011091,0.3271095,0.01050083,0.005869003,0.0004543907,0.002574223,0.02553341],"genre_scores_gemma":[0.07511103,0.003439542,0.8705558,0.03698321,0.001966796,0.004083449,0.001248386,0.001486034,0.005125789],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.3122311,"threshold_uncertainty_score":0.3850366,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1160671162138862,"score_gpt":0.4474668136495942,"score_spread":0.331399697435708,"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."}}