{"id":"W3156723047","doi":"10.1186/s13073-021-00858-2","title":"A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch","year":2021,"lang":"en","type":"article","venue":"Genome Medicine","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":125,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Agency of Canada","funders":"National Institute of Allergy and Infectious Diseases; European Centre for Disease Prevention and Control; Conselleria de Sanitat Universal i Salut Pública; Wellcome Trust; Wellcome; World Health Organization; National Institute for Health and Care Research; Li Ka Shing Foundation; U.S. Department of Veterans Affairs; National Institutes of Health; National Science Foundation","keywords":"Neisseria gonorrhoeae; Antibiotic resistance; Men who have sex with men; Public health; Gonorrhea; Genomics; Medicine; Molecular epidemiology; Azithromycin; Biology; Genetics; Genome; Virology; Genotype; Antibiotics; Syphilis","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":[0.002042895,0.0001758395,0.0006217529,0.0001590745,0.0005035911,0.000002585058,0.0001964707,0.0002249676,0.0002923006],"category_scores_gemma":[0.00200696,0.0001590163,0.00007694679,0.0002273456,0.0009121887,0.00004205612,0.0002372809,0.0004882845,0.00002983802],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000137715,"about_ca_system_score_gemma":0.00009272841,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001292893,"about_ca_topic_score_gemma":0.0001843993,"domain_scores_codex":[0.9971454,0.001400749,0.0005893272,0.0004313799,0.00001768241,0.0004155017],"domain_scores_gemma":[0.9976257,0.001094859,0.0002193517,0.0007245868,0.0002908501,0.00004465192],"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":[0.0004826849,0.0001048584,0.01291457,0.0002049491,0.0001879766,0.000001200312,0.001141061,0.00002507869,0.9785485,0.0002313608,0.005528602,0.000629214],"study_design_scores_gemma":[0.003808364,0.0008848961,0.391374,0.0001360797,0.0001652665,0.0005478058,0.000984057,0.000006853165,0.05478969,0.0005486479,0.546542,0.000212329],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9822053,0.01097443,0.0008121979,0.003722679,0.0003648059,0.0005359861,0.0003271659,0.00004198342,0.001015454],"genre_scores_gemma":[0.9861073,0.0009292081,0.0007278413,0.0002619352,0.0002050199,0.00007122586,0.001390193,0.000034695,0.01027254],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9237587,"threshold_uncertainty_score":0.6484496,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05317493685720472,"score_gpt":0.3076978842285473,"score_spread":0.2545229473713426,"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."}}