{"id":"W3118498167","doi":"10.1093/jac/dkaa552","title":"<i>Neisseria gonorrhoeae</i>Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions","year":2020,"lang":"en","type":"article","venue":"Journal of Antimicrobial Chemotherapy","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":38,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Generalitat Valenciana","keywords":"Neisseria gonorrhoeae; Multilocus sequence typing; Biology; Typing; Antibiotic resistance; Genetics; Phylogenetics; Microbiology; Virology; Genotype; Gene","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0005593287,0.0004778902,0.000883493,0.0002900136,0.0007175001,0.0001944953,0.0003409584,0.0002994696,0.00005647607],"category_scores_gemma":[0.0001973152,0.0004322737,0.0002016776,0.0004634451,0.0008956132,0.000474794,0.00006858248,0.0006997145,0.000005647891],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001525679,"about_ca_system_score_gemma":0.000419112,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002156944,"about_ca_topic_score_gemma":0.0000930427,"domain_scores_codex":[0.9973028,0.0002582756,0.000986031,0.0007734845,0.00007093451,0.0006084941],"domain_scores_gemma":[0.9974058,0.0002337695,0.001083697,0.0003146534,0.0008283376,0.000133702],"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":[0.007079456,0.0002594624,0.002963311,0.0004729883,0.0005547297,0.000007891199,0.0007847484,0.00005382291,0.9642747,0.0001446035,0.02326247,0.000141783],"study_design_scores_gemma":[0.01119108,0.001286855,0.01309119,0.0007357355,0.0002845134,0.001185787,0.0003129443,0.00006453789,0.8242679,0.00006334499,0.146566,0.000950147],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9845611,0.001871931,0.006469923,0.00475566,0.0004158528,0.001277908,0.0005243639,0.00007286261,0.00005037751],"genre_scores_gemma":[0.9886495,0.00223326,0.005868181,0.002164849,0.0004893249,0.00001585468,0.0001542422,0.0001051083,0.000319688],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1400069,"threshold_uncertainty_score":0.9998129,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02644018283061539,"score_gpt":0.279471795723976,"score_spread":0.2530316128933606,"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."}}