{"id":"W7125835393","doi":"10.17504/protocols.io.5qpvo1n37g4o/v1","title":"Variant Effect Mapping Protocol Collection v1","year":2025,"lang":"","type":"article","venue":"","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; National Institutes of Health","keywords":"Workflow; Scalability; Protocol (science); Function (biology); Protein function; Measure (data warehouse); Data collection; Human disease","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":[0.006016885,0.00317001,0.003235451,0.005837193,0.003145525,0.003533331,0.004401627,0.002376524,0.2368031],"category_scores_gemma":[0.01653982,0.004195055,0.002389194,0.004147348,0.001041331,0.00208143,0.003669138,0.004255944,0.1633109],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001225511,"about_ca_system_score_gemma":0.004619226,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00301137,"about_ca_topic_score_gemma":0.006034406,"domain_scores_codex":[0.9930379,0.00140265,0.001435753,0.001466956,0.001951456,0.0007053854],"domain_scores_gemma":[0.9920011,0.002027372,0.0003785566,0.002963697,0.002266389,0.0003629383],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00238597,0.0004639586,0.002399492,0.006729729,0.000276712,0.001237945,0.0006950119,0.002604192,0.2186184,0.01671695,0.6268928,0.1209789],"study_design_scores_gemma":[0.0003224773,0.0003402334,0.002079909,0.0006045342,0.0001090739,0.001076033,0.0001437633,0.001607735,0.09190477,0.007989538,0.8936138,0.0002081849],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"protocol","genre_scores_codex":[0.0074978,0.002290621,0.3368289,0.0009416104,0.001366676,0.01836279,0.5158914,0.06228179,0.05453845],"genre_scores_gemma":[0.01027189,0.00201601,0.2157251,0.001350606,0.0001776267,0.03862474,0.6720964,0.01838683,0.04135085],"genre_candidate":"protocol","genre_consensus":null,"teacher_disagreement_score":0.2368031,"threshold_uncertainty_score":0.7921852,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004567425092317002,"score_gpt":0.2580496753021155,"score_spread":0.2534822502097985,"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."}}