{"id":"W2796622087","doi":"10.1099/mgen.0.000175","title":"Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Pneumonia and Respiratory Infections","field":"Medicine","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"Provincial Laboratory of Public Health; University of British Columbia; BC Centre for Disease Control; University of Alberta Hospital; Alberta Hospital Edmonton; University of Alberta","funders":"","keywords":"Biology; Streptococcus pneumoniae; Genome; Clade; Comparative genomics; Phylogenetic tree; Genetics; Genomics; Microbiology; Gene; Bacteria","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0004044225,0.0004512355,0.0007651188,0.0004470911,0.0002692035,0.0001108398,0.0002414274,0.0002420421,0.00004038434],"category_scores_gemma":[0.000653338,0.0004333165,0.0001684131,0.0004553559,0.0002831326,0.0001264337,0.0003430392,0.0002964817,0.0002332542],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003306336,"about_ca_system_score_gemma":0.000344566,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009951286,"about_ca_topic_score_gemma":0.0001211994,"domain_scores_codex":[0.9974701,0.000160066,0.0007645487,0.0007418559,0.0001796587,0.0006837999],"domain_scores_gemma":[0.9974799,0.000539473,0.0001995982,0.0007456152,0.0003073487,0.0007280713],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00008140117,0.0001566106,0.06560125,0.00006428896,0.0001502832,0.0000299103,0.001469217,0.0002208733,0.9213703,0.00002231293,0.001320685,0.009512866],"study_design_scores_gemma":[0.001896888,0.004807909,0.39473,0.0003806862,0.0009994165,0.0001200104,0.0002790393,0.0001614401,0.4401869,0.00009911355,0.155076,0.001262507],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9870167,0.00002349701,0.007899418,0.001370135,0.0003454544,0.002751495,0.0004122969,0.00009297962,0.00008802932],"genre_scores_gemma":[0.993384,0.00004700648,0.003967217,0.001324624,0.0006643269,0.0001166086,0.00002914686,0.0001111864,0.0003558807],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4811834,"threshold_uncertainty_score":0.9998119,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05584724043814365,"score_gpt":0.2893367749569121,"score_spread":0.2334895345187684,"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."}}