{"id":"W3116451876","doi":"10.1093/gigascience/giaa149","title":"GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci","year":2020,"lang":"en","type":"article","venue":"GigaScience","topic":"Genetic Mapping and Diversity in Plants and Animals","field":"Biochemistry, Genetics and Molecular Biology","cited_by":327,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"Agriculture and Agri-Food Canada; Beef Cattle Research Council; Beef Farmers of Ontario; Alberta Beef Producers","keywords":"Annotation; Computational biology; Livestock; R package; Genome; Computer science; Biology; Genomic selection; Data science; Genetics; Bioinformatics; Information retrieval; Gene; Genotype; Single-nucleotide polymorphism","routes":{"ca_aff":true,"ca_fund":true,"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":[0.005617908,0.003934533,0.003282838,0.003203879,0.0008210118,0.003191093,0.004301017,0.001321494,0.0475965],"category_scores_gemma":[0.01804183,0.002103502,0.003905721,0.002549385,0.001083576,0.002165275,0.004126807,0.003365555,0.03197743],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000715228,"about_ca_system_score_gemma":0.002858317,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002984449,"about_ca_topic_score_gemma":0.0032503,"domain_scores_codex":[0.9970167,0.001190422,0.0002905494,0.0007386378,0.0004961032,0.0002675406],"domain_scores_gemma":[0.9926378,0.004966325,0.0007037593,0.0008606216,0.0005255045,0.000306008],"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":[0.003077949,0.0001750901,0.01391491,0.01124361,0.005641954,0.001442191,0.001326606,0.0131159,0.02180446,0.0194731,0.7800387,0.1287455],"study_design_scores_gemma":[0.00184695,0.0004057753,0.02038382,0.001579261,0.002151183,0.001502402,0.0003386712,0.07875302,0.02097539,0.05926377,0.8122143,0.0005853968],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.005955829,0.002006145,0.3599567,0.0008769661,0.000454653,0.0005400163,0.1960717,0.4290591,0.005078896],"genre_scores_gemma":[0.05575788,0.001864747,0.4880635,0.001684323,0.0002727681,0.005087744,0.2172412,0.2233729,0.006654951],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.0475965,"threshold_uncertainty_score":0.1592261,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04584508785596735,"score_gpt":0.2726123492925291,"score_spread":0.2267672614365618,"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."}}