{"id":"W4410153702","doi":"10.1371/journal.pbio.3003157","title":"A standardized nomenclature for the rods and cones of the vertebrate retina","year":2025,"lang":"en","type":"article","venue":"PLoS Biology","topic":"Retinal Development and Disorders","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"H2020 European Research Council; Biotechnology and Biological Sciences Research Council; National Eye Institute; Wellcome Trust; Lister Institute of Preventive Medicine; Leverhulme Trust; UK Research and Innovation; McKnight Foundation","keywords":"Biology; Vertebrate; Opsin; Nomenclature; Rhodopsin; Evolutionary biology; Retina; Gene; Genetics; Neuroscience; Taxonomy (biology); Retinal; Zoology","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":[0.0001144549,0.00007039344,0.0001027136,0.00001249773,0.00008844849,0.000005395004,0.0001456173,0.0000996243,0.000005336777],"category_scores_gemma":[0.0001668987,0.00003604903,0.00004800562,0.00005679419,0.0001906532,7.155454e-7,0.0001049833,0.0000417537,2.161385e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000002551166,"about_ca_system_score_gemma":0.00006333789,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003343863,"about_ca_topic_score_gemma":0.00001589731,"domain_scores_codex":[0.9995819,0.00004106211,0.0001032508,0.0001447767,0.00002447425,0.0001045659],"domain_scores_gemma":[0.9996765,0.00005004233,0.00004556703,0.0001604324,0.00005759031,0.000009881386],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0008090244,0.00004175923,0.0708499,0.00009100376,0.0003618285,1.093101e-7,0.0001168303,0.00000127338,0.8975752,0.01753633,0.008631503,0.003985217],"study_design_scores_gemma":[0.002700818,0.0004486005,0.0380486,0.00005698327,0.0001529797,0.00000309963,0.0002394389,0.0001449309,0.5804925,0.01938638,0.358071,0.0002546529],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.987316,0.004124216,0.001315602,0.003984357,0.0002173535,0.0004648044,0.00004149287,0.000004957957,0.002531272],"genre_scores_gemma":[0.9975853,0.0005166035,0.0003268622,0.000555078,0.00002497042,0.00004339174,0.00002228819,0.000004107112,0.0009214203],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3494395,"threshold_uncertainty_score":0.1470037,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006111955865747709,"score_gpt":0.2491778418792476,"score_spread":0.2430658860134999,"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."}}