{"id":"W4414351194","doi":"10.1186/s13326-026-00350-z","title":"Representing Dental Caries and Dysbiosis within the Oral Microbiome in the Oral Health and Disease Ontology","year":2025,"lang":"en","type":"preprint","venue":"Journal of Biomedical Semantics","topic":"Oral microbiology and periodontitis research","field":"Dentistry","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"","keywords":"Dysbiosis; Oral Microbiome; Oral health; Disease; Microbiome; Ontology; Metagenomics","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":[0.002842381,0.0002601343,0.0007485726,0.0003112588,0.0003167146,0.0002821047,0.0007787416,0.0004214846,0.00003466741],"category_scores_gemma":[0.001178537,0.0001456993,0.0001701499,0.0002833991,0.001679846,0.00007455281,0.001242789,0.002215841,0.000003046069],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008074089,"about_ca_system_score_gemma":0.0008463622,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009144637,"about_ca_topic_score_gemma":0.002589024,"domain_scores_codex":[0.9965304,0.001282216,0.001021147,0.0003518787,0.0003798618,0.0004344591],"domain_scores_gemma":[0.9980357,0.0005218567,0.0006313234,0.0003563625,0.0001162791,0.0003385055],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001185342,0.0007822118,0.9089226,0.002756439,0.0009602341,0.004294167,0.006127558,0.00000777012,0.001690994,0.001188475,0.06299493,0.00908925],"study_design_scores_gemma":[0.008511915,0.001598817,0.8526795,0.006941271,0.001113463,0.01586539,0.01710512,0.001681143,0.0003379664,0.01539675,0.07719958,0.001569083],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9523061,0.01264616,0.0001645539,0.03252985,0.001727297,0.0003427801,0.0002559897,0.000007996739,0.00001929977],"genre_scores_gemma":[0.9953551,0.001547282,0.0006430278,0.001797128,0.0002787779,0.000005099643,0.00006939069,0.00001212347,0.0002921157],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05624312,"threshold_uncertainty_score":0.962685,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03735955026029671,"score_gpt":0.3642590398067753,"score_spread":0.3268994895464786,"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."}}