{"id":"W4232756746","doi":"10.31219/osf.io/3dybg","title":"A primer and discussion on DNA-based microbiome data and related bioinformatics analyses","year":2021,"lang":"en","type":"preprint","venue":"","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"","keywords":"Microbiome; Metagenomics; Computational biology; Data science; Shotgun sequencing; Profiling (computer programming); Human Microbiome Project; DNA sequencing; Biology; Computer science; Human microbiome; Bioinformatics; Genetics; 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":[0.01540234,0.001436559,0.001220928,0.004058698,0.003066054,0.006126002,0.002603329,0.006855871,0.01340822],"category_scores_gemma":[0.03716109,0.0007212322,0.001983889,0.005563146,0.006413622,0.008209336,0.004995105,0.01222323,0.009323221],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002022152,"about_ca_system_score_gemma":0.002348278,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001365187,"about_ca_topic_score_gemma":0.0009501635,"domain_scores_codex":[0.9899647,0.005329567,0.001037695,0.001042488,0.002313672,0.000311951],"domain_scores_gemma":[0.9669823,0.02730167,0.00108145,0.001374831,0.002373478,0.0008863137],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.0001595212,0.000112777,0.00208455,0.002313077,0.00007365138,0.001437723,0.002136404,0.00176513,0.004780135,0.5156314,0.3703397,0.09916584],"study_design_scores_gemma":[0.000008310254,0.00003252176,0.0006880178,0.0006716599,0.000006606514,0.0007590684,0.0002570712,0.0006010503,0.0009683915,0.09132944,0.9046332,0.00004468386],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":"theoretical_or_conceptual","genre_codex":"commentary","genre_gemma":"methods","genre_scores_codex":[0.003296342,0.1105632,0.2739938,0.4880688,0.09484436,0.0004186592,0.004296225,0.001393234,0.02312536],"genre_scores_gemma":[0.03496811,0.1244589,0.2995166,0.3439043,0.1454944,0.002163287,0.004189825,0.002876219,0.04242828],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.01540234,"threshold_uncertainty_score":0.08145636,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04428475431832332,"score_gpt":0.3443520657376533,"score_spread":0.30006731141933,"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."}}