{"id":"W2229090536","doi":"10.1093/nar/gkv1269","title":"EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems","year":2015,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":197,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children","funders":"Austrian Science Fund","keywords":"Biology; RefSeq; Secretion; Bacterial genome size; Genome; Annotation; Computational biology; Metagenomics; Bacterial protein; Genome project; Bacteria; Genetics; Bioinformatics; Gene; Biochemistry","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":[0.001078649,0.0001338456,0.0002095635,0.0001187968,0.0001329283,0.00009376775,0.0001214646,0.0001807548,0.000004485441],"category_scores_gemma":[0.0009775237,0.0001138517,0.00002702757,0.0001519145,0.0003224788,0.00001741184,0.0002831246,0.0001461538,0.000001265736],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000337119,"about_ca_system_score_gemma":0.0001127616,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001224467,"about_ca_topic_score_gemma":0.00002816707,"domain_scores_codex":[0.9985825,0.0002110943,0.0001671767,0.0003664008,0.000335176,0.0003376427],"domain_scores_gemma":[0.9985998,0.00007558126,0.00005719631,0.0002125851,0.0009220695,0.0001327902],"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":[0.001908038,0.00003419938,0.001447827,0.0001966109,0.00009268126,7.287343e-7,0.0002991596,0.000001574119,0.9927989,0.00006998883,0.002141739,0.001008504],"study_design_scores_gemma":[0.0128176,0.01178089,0.09855222,0.0003013427,0.00006164338,0.00005473453,0.002434104,0.002469671,0.8327292,0.0004622904,0.03761334,0.0007229591],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9967694,0.0006243459,0.0006464575,0.0002198507,0.00009908324,0.001395957,0.00009984375,0.000009965725,0.0001351128],"genre_scores_gemma":[0.9980794,0.0001040295,0.0007884679,0.00001138681,0.0003184524,0.0001892143,0.0002835034,0.00002574191,0.000199832],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1600697,"threshold_uncertainty_score":0.4642738,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03905644916540325,"score_gpt":0.3346384994608168,"score_spread":0.2955820502954135,"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."}}