{"id":"W2099753867","doi":"10.1186/1471-2105-12-491","title":"MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects","year":2011,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2312,"is_retracted":false,"has_abstract":true,"ca_institutions":"Ontario Institute for Cancer Research","funders":"Division of Integrative Organismal Systems; National Institute of General Medical Sciences; National Human Genome Research Institute; University of Utah; Agricultural Research Service; San Francisco State University; Michigan State University; College of Engineering, Michigan State University; U.S. Department of Agriculture; National Institutes of Health; National Science Foundation","keywords":"Annotation; Genome; Genome project; Gene Annotation; Computer science; DNA sequencing; Pipeline (software); Genome browser; Computational biology; Genomics; Database; Data mining; Biology; Gene; Genetics; Artificial intelligence","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":[0.009493947,0.005252019,0.00257325,0.007264455,0.003261194,0.006893245,0.008182982,0.003210953,0.02858165],"category_scores_gemma":[0.01963092,0.004022828,0.003421888,0.008139729,0.001165009,0.00572265,0.007175013,0.006050323,0.02254083],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001860878,"about_ca_system_score_gemma":0.004140984,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00176904,"about_ca_topic_score_gemma":0.001787698,"domain_scores_codex":[0.9952631,0.0007036352,0.0004977278,0.001448283,0.001729638,0.000357697],"domain_scores_gemma":[0.992574,0.002794777,0.001132449,0.001381677,0.001189764,0.0009272904],"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":[0.00307706,0.0003298643,0.004786778,0.003769115,0.0006788102,0.001574977,0.001446484,0.006630694,0.04446607,0.01229154,0.7771792,0.1437694],"study_design_scores_gemma":[0.001223398,0.0003216167,0.006387158,0.0004456725,0.0003929197,0.001425287,0.0004110525,0.049209,0.08549716,0.03102177,0.822902,0.0007630424],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.005469632,0.0007947944,0.4306002,0.001280804,0.0007997465,0.001102699,0.1048083,0.4494049,0.005738907],"genre_scores_gemma":[0.02731824,0.0008500857,0.6304623,0.001303529,0.0003326541,0.005132054,0.2519807,0.07469785,0.007922563],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.02858165,"threshold_uncertainty_score":0.09561515,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04623520706017015,"score_gpt":0.2460322174434468,"score_spread":0.1997970103832766,"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."}}