{"id":"W4408187354","doi":"10.1093/genetics/iyaf027","title":"The Unified Phenotype Ontology : a framework for cross-species integrative phenomics","year":2025,"lang":"en","type":"article","venue":"Genetics","topic":"Biomedical Text Mining and Ontologies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Basic Energy Sciences; Takeda Canada; Biotechnology and Biological Sciences Research Council; Office of Science; National Institutes of Health; Norges Idrettshøgskole; GlaxoSmithKline foundation; National Human Genome Research Institute; Wellcome Trust; Eunice Kennedy Shriver National Institute of Child Health and Human Development; U.S. Department of Energy; European Bioinformatics Institute; Centers for Disease Control and Prevention; Sanofi Australia; Biogen; Celgene; Office of the Director","keywords":"Phenomics; Ontology; Phenome; Biology; Data integration; Phenotypic trait; Controlled vocabulary; Computational biology; Open Biomedical Ontologies; Representation (politics); Biological data; Data science; Organism; Computer science; Vocabulary; Phenotype; Ontology-based data integration; Bioinformatics; Genomics; Data mining; Information retrieval; Genetics; Genome; Ontology alignment; Semantic Web; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01520598,0.001772991,0.001912317,0.009435434,0.003366594,0.009183098,0.007539513,0.003063042,0.003501239],"category_scores_gemma":[0.01417059,0.00162879,0.00543232,0.009330367,0.004551833,0.01479536,0.008928536,0.006689853,0.002153443],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.004812276,"about_ca_system_score_gemma":0.01192767,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02448571,"about_ca_topic_score_gemma":0.02344528,"domain_scores_codex":[0.9926869,0.002414926,0.001370507,0.001111879,0.002034307,0.0003815854],"domain_scores_gemma":[0.9925084,0.002741343,0.0008026175,0.001956893,0.00131091,0.000679883],"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":[0.00006353948,0.0001257989,0.001266737,0.0007749704,0.000185154,0.0008138496,0.002279449,0.01355137,0.002506258,0.8624665,0.01903761,0.0969287],"study_design_scores_gemma":[0.00003529661,0.00004654187,0.0008326168,0.000839999,0.0001321149,0.0007134583,0.0009083378,0.05789781,0.001750883,0.5846664,0.3520471,0.0001294761],"study_design_candidate":"theoretical_or_conceptual","study_design_consensus":"theoretical_or_conceptual","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.0007508449,0.0004311108,0.9891722,0.001182461,0.0001126056,0.0003406845,0.001632809,0.003046677,0.003330501],"genre_scores_gemma":[0.01203411,0.001277183,0.9760298,0.0006721098,0.0001140779,0.000909146,0.006605529,0.0007845255,0.001573481],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02448571,"threshold_uncertainty_score":0.08041787,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02122785670023918,"score_gpt":0.3328977548537405,"score_spread":0.3116698981535013,"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."}}