{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.006562349,0.0007194363,0.0007002278,0.007159158,0.002203198,0.00451845,0.001776752,0.001814736,0.002688861],"category_scores_gemma":[0.01368367,0.0004915769,0.002462091,0.007137154,0.002769014,0.01062701,0.00441512,0.002509314,0.0006864255],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.004892542,"about_ca_system_score_gemma":0.008778988,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02203913,"about_ca_topic_score_gemma":0.02467177,"domain_scores_codex":[0.995604,0.001532793,0.0008527404,0.0005284764,0.001172864,0.0003091432],"domain_scores_gemma":[0.9903011,0.005752974,0.000921543,0.0009706407,0.001550237,0.000503423],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001796059,0.0001511562,0.01448887,0.004752497,0.0003203904,0.00134779,0.01539575,0.006193514,0.005763226,0.7242314,0.03733956,0.1898364],"study_design_scores_gemma":[0.00003477127,0.00004830146,0.00691742,0.00305192,0.000384259,0.001454033,0.005414754,0.01191262,0.001966738,0.2533186,0.7153426,0.0001539254],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.06946559,0.02589894,0.7697025,0.02360755,0.002389633,0.001543926,0.0262163,0.00334171,0.07783382],"genre_scores_gemma":[0.2027573,0.01582721,0.7440979,0.00386094,0.0005161933,0.00129867,0.02458849,0.0005540614,0.006499143],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02203913,"threshold_uncertainty_score":0.04382169,"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."}}