{"id":"W4319447645","doi":"10.1016/j.ajog.2022.11.156","title":"Femmicro16S: open source tools for annotation and meta-analysis of 16s vaginal microbiome data","year":2023,"lang":"en","type":"article","venue":"American Journal of Obstetrics and Gynecology","topic":"Reproductive tract infections research","field":"Immunology and Microbiology","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Calgary","funders":"","keywords":"Microbiome; Pipeline (software); Annotation; Medicine; Open source; Computational biology; Data science; World Wide Web; Bioinformatics; Computer science; Biology; Software","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":[0.007042716,0.004426032,0.004027959,0.008757492,0.002026524,0.004115734,0.003422485,0.002132081,0.01893311],"category_scores_gemma":[0.01871588,0.002105964,0.00667677,0.006355055,0.000753253,0.002427726,0.006059116,0.002682758,0.01241005],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008461943,"about_ca_system_score_gemma":0.004744961,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00572176,"about_ca_topic_score_gemma":0.009883406,"domain_scores_codex":[0.9967567,0.0007900307,0.0004596665,0.001219169,0.0004752865,0.0002990388],"domain_scores_gemma":[0.9949036,0.002796501,0.0006266103,0.0008354011,0.000471042,0.0003668316],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.008887398,0.0007515876,0.0849756,0.04937852,0.02962231,0.002281083,0.007491101,0.02212626,0.1511129,0.01689539,0.3854259,0.2410519],"study_design_scores_gemma":[0.001830944,0.0009231347,0.05600157,0.004327944,0.009209273,0.001263966,0.001737533,0.05694006,0.05472422,0.04207921,0.7696207,0.001341467],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"dataset","genre_gemma":"software","genre_scores_codex":[0.02541502,0.006701582,0.1396971,0.0005804621,0.0009846309,0.0004987963,0.656949,0.1655531,0.003620293],"genre_scores_gemma":[0.07888626,0.003100176,0.3412394,0.0009748719,0.0002693383,0.002988022,0.5319878,0.03715853,0.003395677],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01893311,"threshold_uncertainty_score":0.06333756,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.160626771872179,"score_gpt":0.3903806180445382,"score_spread":0.2297538461723592,"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."}}