{"id":"W2120419610","doi":"10.1038/ng.2214","title":"Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing","year":2012,"lang":"en","type":"article","venue":"Nature Genetics","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":312,"is_retracted":false,"has_abstract":false,"ca_institutions":"BC Centre for Disease Control","funders":"National Institute for Health and Care Research; Wellcome Trust","keywords":"Biology; Chlamydia trachomatis; Lymphogranuloma venereum; Phylogenetic tree; Trachoma; Genetics; Phylogenetics; Multilocus sequence typing; Genome; Whole genome sequencing; Chlamydiaceae; Evolutionary biology; Virology; Computational biology; Genotype; 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":[0.0003310838,0.0003063485,0.0003924009,0.0009397899,0.0004431251,0.0007056355,0.0002599008,0.0005749777,0.001078323],"category_scores_gemma":[0.0008428615,0.0001805239,0.0004201178,0.001320681,0.0002941422,0.0002943366,0.0004706983,0.0007142278,0.000286619],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001990168,"about_ca_system_score_gemma":0.0002513516,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002222286,"about_ca_topic_score_gemma":0.005602261,"domain_scores_codex":[0.9997076,0.00004428955,0.00001799165,0.00009864975,0.00005332541,0.00007811611],"domain_scores_gemma":[0.9994456,0.0001770319,0.0001316931,0.00007399872,0.00006328975,0.0001083744],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0008329813,0.0001053447,0.1486843,0.0001558545,0.0003002715,0.0001867883,0.0004613984,0.0002950959,0.8296379,0.0001872555,0.0005803361,0.01857251],"study_design_scores_gemma":[0.00001179388,0.0001508647,0.9812534,0.00002194514,0.0001702195,0.0007547342,0.0004124625,0.001090997,0.01357331,0.0002152246,0.002330465,0.00001458123],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9951625,0.0006816983,0.001216246,0.0001372889,0.00001690322,0.000006497082,0.0022536,0.00003800955,0.0004872349],"genre_scores_gemma":[0.9933609,0.000382535,0.002005799,0.0001906088,0.00001459865,0.00000581419,0.003719904,0.00003391842,0.0002858635],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002222286,"threshold_uncertainty_score":0.004418731,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06388679883420732,"score_gpt":0.3726815488172143,"score_spread":0.3087947499830069,"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."}}