{"meta":{"page":1,"per_page":50,"max_per_page":100,"total":232,"total_is_capped":false,"direct_labels_cover":0,"predictions_cover":232,"direct_label_status":"direct model label, unvalidated","prediction_status":"machine_predicted_unvalidated (Codex and Gemma teacher distillation)","score_status":"score_only:v0-immature-baseline (scores rank; they never assert a category)","snapshot":{"source":"OpenAlex, pinned release, all 482 partitions","release":"2026-06-24","frame_built":"2026-07-12"},"query_hash":"b926328eed30","filters":{"venue":"Nature Protocols"}},"results":[{"id":"W1979973356","doi":"10.1038/nprot.2007.521","title":"Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances","year":2008,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Antimicrobial Peptides and Activities","field":"Immunology and Microbiology","cited_by":6078,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"","keywords":"Antimicrobial; Minimum inhibitory concentration; Agar; Agar dilution; Bacteria; Dilution; Bacterial growth; Agar plate; Microbiology; Minimum bactericidal concentration; Serial dilution; Chromatography; Nutrient agar; Chemistry; Microtiter plate; Agar Dilution Method; Food science; Biology; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.02222632366661649,"gpt":0.3142846630623062,"spread":0.2920583393956898,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002521731,0.0001532422,0.0002581294,0.00004109728,0.0002448776,0.00001387003,0.0001471609,0.0003288061,0.00003489833],"category_scores_gemma":[0.00007946687,0.0001064364,0.00006418928,0.0001125781,0.0004556256,0.0001303328,0.00006083673,0.0003972373,0.00000832527],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001927548,"about_ca_system_score_gemma":0.00006035507,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002627118,"about_ca_topic_score_gemma":0.00002004658,"domain_scores_codex":[0.9990792,0.0001712309,0.0002601777,0.0002327189,0.00003550249,0.0002211546],"domain_scores_gemma":[0.9994299,0.0001401448,0.000163402,0.0001616398,0.000087792,0.00001705481],"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":[0.0003869358,0.00005229854,0.001198534,0.00004154231,0.00002961309,0.00000177238,0.000646635,0.000002039881,0.986093,0.0002436446,0.006330089,0.004973874],"study_design_scores_gemma":[0.000709558,0.0001783754,0.004217468,0.0001140337,0.0000130585,0.00009164281,0.00006064387,0.00000252184,0.9647351,0.00002773077,0.029718,0.0001318839],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9760857,0.0007062036,0.0007954688,0.0004189907,0.000254073,0.02129995,0.00004793577,0.00004037417,0.0003513267],"genre_scores_gemma":[0.9920152,0.00002470963,0.004307765,0.0004729526,0.00009444141,0.002653255,0.00001690582,0.00001239595,0.0004023701],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02338791,"threshold_uncertainty_score":0.4340349,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2045949302","doi":"10.1038/nprot.2009.97","title":"Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt","year":2009,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Gene expression and cancer classification","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4605,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"National Cancer Institute; Ontario Institute for Cancer Research; University of California, Santa Cruz","keywords":"Ensembl; Bioconductor; Computer science; Identifier; Computational biology; R package; Genomics; Data mining; Data integration; Genome; Data science; Biology; Gene; Genetics; Programming language","retraction":null,"screen_n_in":null,"score":{"opus":0.02574701164941351,"gpt":0.3351561014281086,"spread":0.3094090897786951,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002125365,0.00008679512,0.000066348,0.00002296514,0.0001049334,0.00003379438,0.0002817834,0.0001318804,0.000005921614],"category_scores_gemma":[0.00003778017,0.00004183931,0.00004647685,0.00008582064,0.00005327906,0.000004822954,0.00002107836,0.0001143444,0.000001016736],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008752427,"about_ca_system_score_gemma":0.00005397313,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000127127,"about_ca_topic_score_gemma":0.000008003552,"domain_scores_codex":[0.9994608,0.00003445338,0.000117974,0.000190963,0.00009835379,0.0000974721],"domain_scores_gemma":[0.9993019,0.00001373634,0.0001324376,0.0004502561,0.00008218323,0.0000194698],"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":[0.000142241,0.00001699158,0.00002863057,0.0000116663,0.00001672664,6.049315e-8,0.00004905394,0.000002366124,0.957191,0.0001899102,0.03549945,0.006851916],"study_design_scores_gemma":[0.0003546956,0.0001394375,0.003890833,0.00002373025,0.00000705416,0.000001707861,0.0001704743,0.00001809766,0.6786815,0.00007668651,0.3165774,0.00005838797],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.4446024,0.003257461,0.1608687,0.02549486,0.0006141639,0.3627046,0.001236545,0.0000801381,0.001141129],"genre_scores_gemma":[0.9723658,0.00000789751,0.0007032587,0.0008651299,0.0001779941,0.02519609,0.0003729404,0.00001019753,0.000300709],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5277634,"threshold_uncertainty_score":0.1706157,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2023535481","doi":"10.1038/nprot.2011.335","title":"Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry","year":2011,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3236,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta","funders":"Biotechnology and Biological Sciences Research Council","keywords":"Chromatography; Metabolome; Mass spectrometry; Metabolomics; Biomarker discovery; Gas chromatography; Gas chromatography–mass spectrometry; Chemistry; Sample preparation; Liquid chromatography–mass spectrometry; Proteomics; Biochemistry","retraction":null,"screen_n_in":null,"score":{"opus":0.01379564892421023,"gpt":0.2859059224097302,"spread":0.27211027348552,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003567367,0.0003063695,0.0005102115,0.0003390263,0.0001518348,0.00002965731,0.0001865091,0.0003462083,0.000008458322],"category_scores_gemma":[0.0001306066,0.0002673556,0.0001521997,0.0004732329,0.00009273469,0.00001139864,0.0001713701,0.0001848817,2.313522e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004572296,"about_ca_system_score_gemma":0.00006276002,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004801368,"about_ca_topic_score_gemma":0.00002671683,"domain_scores_codex":[0.9984294,0.00003356918,0.0003375005,0.0005832808,0.0001671584,0.000449136],"domain_scores_gemma":[0.9991514,0.00001575331,0.0001993518,0.0002996371,0.0001883339,0.0001455298],"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":[0.0006942988,0.0001169629,0.02117652,0.0005399821,0.0002826807,9.059709e-7,0.0001284266,5.635622e-7,0.9747502,0.002180832,0.00006677401,0.00006189092],"study_design_scores_gemma":[0.001521533,0.001049761,0.008075912,0.00008479432,0.00009393683,0.00002132357,0.0001656987,0.0001299,0.9851522,0.0006096591,0.002750985,0.0003442253],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9669595,0.002801873,0.002852697,0.00003740986,0.00005392252,0.02693601,0.0001672735,0.00002363126,0.0001676803],"genre_scores_gemma":[0.8396689,0.0001988958,0.1466385,0.000125913,0.0001409282,0.01315218,0.00001399758,0.00004892514,0.00001173612],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1437858,"threshold_uncertainty_score":0.9999779,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2038591876","doi":"10.1038/nprot.2007.13","title":"High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2955,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Manitoba","funders":"","keywords":"Transformation (genetics); Transformation efficiency; Yeast; Saccharomyces cerevisiae; PEG ratio; Yield (engineering); DNA; Lithium (medication); Computational biology; Chemistry; Combinatorial chemistry; Biology; Biochemistry; Materials science; Gene; Agrobacterium","retraction":null,"screen_n_in":null,"score":{"opus":0.01031908455211157,"gpt":0.3798412857771429,"spread":0.3695222012250313,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005935399,0.0001402078,0.0001024311,0.00003693205,0.0001090483,0.00003139278,0.0002011786,0.0003244289,0.00001079633],"category_scores_gemma":[0.00004618685,0.0001017413,0.00007965923,0.0001510815,0.00002670846,0.000004464719,0.00003272118,0.0002897821,0.000001709257],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001717807,"about_ca_system_score_gemma":0.00004177776,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009407378,"about_ca_topic_score_gemma":0.00001897343,"domain_scores_codex":[0.9991282,0.0000352109,0.0001956311,0.0002058478,0.0001772463,0.0002579237],"domain_scores_gemma":[0.9995238,0.00001121991,0.00004797302,0.0002799988,0.0000795903,0.00005744441],"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":[0.00007050154,0.00002850397,0.0000720126,0.00004667417,0.00002123745,0.000002259997,0.0002194106,0.002274039,0.9885973,0.0004846524,0.0002542085,0.007929156],"study_design_scores_gemma":[0.0004012634,0.00008671406,0.0006528438,0.00002461639,0.00001315324,0.00002325715,0.00008271969,0.0007210002,0.8993797,0.00004787456,0.09841193,0.0001549839],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.08188213,0.0002919158,0.890512,0.0001391409,0.0003327321,0.02573728,0.00002667483,0.00003194026,0.001046141],"genre_scores_gemma":[0.9803445,0.000003116469,0.01429795,0.0002678854,0.0005577658,0.00425625,0.0000291227,0.00002997424,0.0002134003],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8984624,"threshold_uncertainty_score":0.414889,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2137531873","doi":"10.1038/nprot.2007.324","title":"Integration of biological networks and gene expression data using Cytoscape","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2574,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto","funders":"National Institute of General Medical Sciences","keywords":"Computational biology; Biological network; Gene regulatory network; Gene ontology; Functional genomics; Gene expression profiling; Computer science; Interaction network; Systems biology; Genomics; Context (archaeology); Bioinformatics; Gene expression; Biology; Gene; Data mining; Genome; Genetics","retraction":null,"screen_n_in":null,"score":{"opus":0.04112985887454766,"gpt":0.3468823061421621,"spread":0.3057524472676144,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005201439,0.000104076,0.0001181998,0.00002349508,0.00004640014,0.00001599746,0.0002287423,0.0005424743,0.000003515731],"category_scores_gemma":[0.00004824726,0.00007639305,0.0000240508,0.00005897635,0.00005757649,0.000006330711,0.0003035491,0.0002223336,1.97896e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004850922,"about_ca_system_score_gemma":0.00001947561,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001902825,"about_ca_topic_score_gemma":0.000006926744,"domain_scores_codex":[0.9992974,0.0000224571,0.0002382047,0.0002146703,0.00007105913,0.0001561966],"domain_scores_gemma":[0.999343,0.00001285036,0.0001360975,0.000403181,0.00005553318,0.00004927081],"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":[0.0001860354,0.00002421038,0.0009845647,0.00001449227,0.00001041534,6.844033e-7,0.00001038319,0.00008053433,0.9857939,0.00009592656,0.0004225318,0.01237632],"study_design_scores_gemma":[0.0008796302,0.0003556467,0.002718348,0.0001424889,0.00001194174,0.00003648152,0.00004440203,0.0175843,0.9590722,0.0002672567,0.01861424,0.0002730514],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.355115,0.001501894,0.6207961,0.000026882,0.0001360152,0.02175951,0.00005148321,0.00001666124,0.0005964018],"genre_scores_gemma":[0.9549238,0.00003639721,0.04369937,0.0001664012,0.0003699725,0.0004362353,0.0003434422,0.00001057688,0.00001379743],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.5998088,"threshold_uncertainty_score":0.4184059,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2000106654","doi":"10.1038/nprot.2007.321","title":"The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Molecular Biology Techniques and Applications","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2442,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Structural Genomics Consortium; University of Toronto","funders":"","keywords":"Fluorescence; Nucleic acid; Fluorescence spectroscopy; Chemistry; Ligand (biochemistry); Biophysics; Peptide; Chromatography; Analytical Chemistry (journal); Biochemistry; Biology; Receptor; Optics","retraction":null,"screen_n_in":null,"score":{"opus":0.02989096235273017,"gpt":0.3479978717118817,"spread":0.3181069093591516,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003570735,0.0001419585,0.0001218208,0.00003796109,0.000187064,0.00004002147,0.0002709985,0.0002983356,0.000005412609],"category_scores_gemma":[0.0002531112,0.00009990436,0.0001014444,0.0001506508,0.00009509424,0.000004583349,0.0001739588,0.0003564748,0.000001270792],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001846863,"about_ca_system_score_gemma":0.00004275837,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001237274,"about_ca_topic_score_gemma":0.00008242736,"domain_scores_codex":[0.9990143,0.00006138844,0.0002367209,0.0003203119,0.000128383,0.0002389321],"domain_scores_gemma":[0.9990269,0.00003074001,0.0001285898,0.0005818965,0.0001554229,0.00007645413],"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":[0.0002209541,0.00004575527,0.0007238418,0.00001601232,0.00002507021,4.55616e-7,0.00001167412,6.581275e-7,0.9858924,0.0001454637,0.0004370605,0.01248064],"study_design_scores_gemma":[0.0001224701,0.0002093466,0.001950199,0.00003581402,0.000005401128,0.000003721865,0.000005447162,0.000004779483,0.8185069,0.000102199,0.1789596,0.0000941596],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8488761,0.00004847705,0.1008488,0.0002433968,0.00004164606,0.04974202,0.00002883056,0.00003509125,0.0001356801],"genre_scores_gemma":[0.9544991,0.000001625926,0.01654164,0.0001100204,0.0001001295,0.02852889,0.00002447644,0.00001883083,0.0001753016],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1785225,"threshold_uncertainty_score":0.4073982,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2910111050","doi":"10.1038/s41596-018-0103-9","title":"Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap","year":2019,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2143,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"SickKids Foundation; Ontario Genomics; Hospital for Sick Children; University of Toronto; Ontario Institute for Cancer Research","funders":"National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Cancer Institute; National Human Genome Research Institute","keywords":"Computational biology; Troubleshooting; Visualization; Protocol (science); Biology; Genomics; Genome; Functional genomics; Genome browser; Bioinformatics; Gene; Computer science; Data mining; Genetics","retraction":null,"screen_n_in":null,"score":{"opus":0.01421578793025818,"gpt":0.3144017545757625,"spread":0.3001859666455043,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003185702,0.0001337805,0.0002139945,0.00007640905,0.00003973761,0.0000375274,0.0001951816,0.0003104239,0.00001174485],"category_scores_gemma":[0.00001876128,0.0001179076,0.00003713057,0.0001927952,0.00003591436,0.00001172045,0.0003759362,0.0001190132,7.193541e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008888919,"about_ca_system_score_gemma":0.00005613084,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006352258,"about_ca_topic_score_gemma":0.000008143657,"domain_scores_codex":[0.9991095,0.00003213738,0.0002678913,0.0003124198,0.0001308136,0.0001472305],"domain_scores_gemma":[0.9991226,0.00001053732,0.000200111,0.0005414619,0.0000714279,0.00005384498],"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":[0.000344833,0.0001826342,0.1727757,0.0006789363,0.001148305,0.000001091539,0.0002150614,0.0003331236,0.8068547,0.002572379,0.001355482,0.01353781],"study_design_scores_gemma":[0.008603241,0.002108712,0.04070874,0.0003839037,0.001222692,0.00004394767,0.0005421771,0.2215761,0.5129488,0.001227126,0.2084741,0.002160564],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8953133,0.001956856,0.0471032,0.000123468,0.0001604617,0.05347426,0.0004124872,0.00002054185,0.001435469],"genre_scores_gemma":[0.9914984,0.00008291652,0.006021835,0.0003198324,0.00009286385,0.0009887459,0.0008280883,0.00001694307,0.0001503956],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2939059,"threshold_uncertainty_score":0.4808133,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2900884817","doi":"10.1038/s41596-018-0082-x","title":"Single-pot, solid-phase-enhanced sample preparation for proteomics experiments","year":2018,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":2013,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia; University of Victoria; Canada's Michael Smith Genome Sciences Centre","funders":"","keywords":"Chaotropic agent; Sample preparation; Chromatography; Proteomics; Lysis; Protein purification; Reagent; Chemistry; Computer science; Materials science; Nanotechnology; Biochemistry","retraction":null,"screen_n_in":null,"score":{"opus":0.03518943859435803,"gpt":0.4472757441547395,"spread":0.4120863055603814,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001082377,0.0002249762,0.0002120002,0.00003702477,0.0002746715,0.00007818499,0.0003348797,0.0004806262,0.0001603786],"category_scores_gemma":[0.0001983938,0.000219718,0.0000921383,0.0001243976,0.00009651911,0.0001743364,0.00006817395,0.0003255265,0.00001213004],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001492143,"about_ca_system_score_gemma":0.00006498852,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002797481,"about_ca_topic_score_gemma":0.000004170069,"domain_scores_codex":[0.9986477,0.000008729192,0.0003468084,0.0004929476,0.0001755933,0.0003281919],"domain_scores_gemma":[0.9986725,0.00006179125,0.000268257,0.0005898138,0.0003257524,0.0000818631],"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":[0.0005383704,0.0003316046,0.000007774389,0.00008527093,0.00001401669,1.061746e-7,0.000123583,0.000002124458,0.9908189,0.002492337,0.001208232,0.004377731],"study_design_scores_gemma":[0.00124187,0.0003727217,4.08568e-7,0.00008934286,0.00000645099,0.000001382965,0.00001306857,0.0004824059,0.8445006,0.01815705,0.1349116,0.0002230665],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"protocol","genre_scores_codex":[0.01594146,0.00001499637,0.8548861,0.000134442,0.00003603607,0.1218233,0.0002430533,0.0005314752,0.006389117],"genre_scores_gemma":[0.1316169,5.699185e-7,0.3870028,0.0001363058,0.0004956319,0.4801132,0.0001210806,0.00004377985,0.0004696953],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.4678833,"threshold_uncertainty_score":0.8959841,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2999175750","doi":"10.1038/s41596-019-0264-1","title":"Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data","year":2020,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1822,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"McGill University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Profiling (computer programming); Computer science; Microbiome; Protocol (science); Data mining; Data science; Metagenomics; Computational biology; Web application; Human Microbiome Project; Bioinformatics; Human microbiome; World Wide Web; Biology; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.3441482971478156,"gpt":0.4542390359973068,"spread":0.1100907388494912,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001426476,0.0001743174,0.0006835677,0.000095583,0.00007871963,0.00002827638,0.0002580796,0.0002607511,0.00005778735],"category_scores_gemma":[0.00006640549,0.0001449459,0.0002398522,0.00035052,0.0001033575,0.000005773858,0.0002374805,0.0001458899,9.062102e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005783309,"about_ca_system_score_gemma":0.0001059457,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001253493,"about_ca_topic_score_gemma":0.00001858561,"domain_scores_codex":[0.998758,0.00006355,0.0003265115,0.0005845813,0.00008191082,0.000185455],"domain_scores_gemma":[0.9989319,0.00004018356,0.0001901475,0.0004763175,0.0002594511,0.0001020296],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001970105,0.00004442721,0.00008753193,0.0002382444,0.02658791,5.70436e-7,0.00001366826,0.0000455445,0.957576,0.0001217662,0.01506638,0.00002095011],"study_design_scores_gemma":[0.00215516,0.0006654929,0.00158811,0.000008539228,0.1714688,0.0000186171,0.0000760262,0.003139894,0.2082631,0.00003845359,0.6119229,0.0006548981],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.09559862,0.02619389,0.4649667,0.01075698,0.0002104946,0.2750883,0.1268837,0.0001468473,0.0001544267],"genre_scores_gemma":[0.6136153,0.00006691879,0.3199546,0.01891742,0.0005337416,0.01435349,0.03214718,0.0001587717,0.0002525559],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.7493129,"threshold_uncertainty_score":0.5910721,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2004326614","doi":"10.1038/nprot.2006.5","title":"The comet assay: a method to measure DNA damage in individual cells","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Carcinogens and Genotoxicity Assessment","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1818,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"BC Cancer Agency","funders":"","keywords":"DNA damage; Comet assay; Biology; DNA; DNA repair; Gel electrophoresis; Population; Molecular biology; Computational biology; Genetics; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.01498018698915863,"gpt":0.3395719441103784,"spread":0.3245917571212198,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001484928,0.0001794806,0.000165936,0.00006137462,0.0001225414,0.0001089558,0.000405418,0.0003964191,0.000009908004],"category_scores_gemma":[0.00006385192,0.0001318416,0.00009613794,0.0002595782,0.00002940906,0.000002794629,0.0002039517,0.0004200631,0.000007609622],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003296182,"about_ca_system_score_gemma":0.0001038846,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004656743,"about_ca_topic_score_gemma":0.001042503,"domain_scores_codex":[0.9984283,0.0002833976,0.0002336632,0.0003722868,0.0003429453,0.000339351],"domain_scores_gemma":[0.999267,0.00004658429,0.00007125892,0.0004455399,0.0001009319,0.00006863278],"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":[0.0001404283,0.0001225033,0.002110583,0.00001787884,0.00002794252,0.000008554468,0.00002615535,0.0001206165,0.9683375,0.0005023486,0.02351354,0.005071957],"study_design_scores_gemma":[0.0005735011,0.0001721684,0.0164012,0.00001968401,0.00000665118,0.000004029162,0.00002450243,0.00001436035,0.592602,0.0002327913,0.3897831,0.0001660068],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.4912069,0.001587928,0.04162556,0.00911597,0.0006704304,0.4284279,0.00089908,0.000143033,0.0263232],"genre_scores_gemma":[0.8605168,0.000002961875,0.02630565,0.002569915,0.0007697127,0.1076219,0.000148974,0.00006609088,0.001997934],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3757355,"threshold_uncertainty_score":0.5376344,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1988579368","doi":"10.1038/nprot.2006.46","title":"The Dimensional Change Card Sort (DCCS): a method of assessing executive function in children","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Child and Animal Learning Development","field":"Psychology","cited_by":1536,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto","funders":"","keywords":"Card sorting; sort; Autism; Psychology; Executive functions; Developmental psychology; Audiology; Cognition; Neuroscience; Computer science; Medicine; Information retrieval","retraction":null,"screen_n_in":null,"score":{"opus":0.0204604965889699,"gpt":0.3714756713197455,"spread":0.3510151747307756,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007113346,0.0001386611,0.000197281,0.00008367347,0.0001270529,0.00003262131,0.0001338868,0.0002622265,0.0000484041],"category_scores_gemma":[0.00004491589,0.00009419558,0.00007407684,0.0002470049,0.0000411208,0.00006844567,0.00005088639,0.0007290028,0.00001305038],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004805112,"about_ca_system_score_gemma":0.00004742346,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001912659,"about_ca_topic_score_gemma":0.00003830892,"domain_scores_codex":[0.9986928,0.0002405662,0.0002638566,0.0003026286,0.000255368,0.0002448554],"domain_scores_gemma":[0.9993847,0.0001658483,0.0001676658,0.0001847185,0.00007347072,0.00002357254],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001068142,0.0006175988,0.8518859,0.00003794167,0.0001945036,0.00001593665,0.001185848,0.00002639704,0.003149072,0.03624016,0.0120258,0.09355269],"study_design_scores_gemma":[0.0008043069,0.00009065988,0.9698741,0.0001137877,0.000009125437,0.00001727769,0.00004869521,0.00000945861,0.0005375778,0.001246171,0.02713289,0.0001159201],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5183913,0.002858406,0.001948249,0.004000867,0.001766564,0.3818564,0.0001020316,0.0004479745,0.08862817],"genre_scores_gemma":[0.9445214,6.510925e-7,0.00415061,0.0004214834,0.0006006947,0.04915428,0.00004127029,0.00003279084,0.001076837],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4261301,"threshold_uncertainty_score":0.3841184,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4283017342","doi":"10.1038/s41596-022-00710-w","title":"Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data","year":2022,"lang":"en","type":"review","venue":"Nature Protocols","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1509,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"McGill Genome Centre; McGill University","funders":"National Institutes of Health; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs; Génome Québec; Genome Canada","keywords":"Metabolomics; Computer science; Protocol (science); Metadata; Exploratory data analysis; Data mining; Data science; Bioinformatics; Biology; World Wide Web; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.1699560688585668,"gpt":0.4521117184338692,"spread":0.2821556495753024,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0009324218,0.0006038771,0.001877845,0.0001146858,0.0001808964,0.00007142105,0.0008838049,0.0007142471,0.00001032095],"category_scores_gemma":[0.0004426336,0.0004786026,0.000386203,0.0004360364,0.00009954206,0.00001521555,0.0009613905,0.0005569182,2.064135e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001131638,"about_ca_system_score_gemma":0.0006202497,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001420525,"about_ca_topic_score_gemma":0.00005096401,"domain_scores_codex":[0.9971905,0.0001820044,0.0008768433,0.001117762,0.0002710909,0.0003617611],"domain_scores_gemma":[0.9975008,0.00003443131,0.001181043,0.001025842,0.0001766614,0.00008116864],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003124601,0.0005036263,0.00002684989,0.01578601,0.003128094,0.000002542098,0.00002151876,0.000009393178,0.003652554,0.004719048,0.0006766897,0.9711612],"study_design_scores_gemma":[0.0008943343,0.0002001129,0.000007229371,0.0004797502,0.002403809,0.00002865388,0.00002518145,0.0005129671,0.0006130043,0.0001309521,0.9942381,0.0004658745],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.000005936714,0.9301611,0.01701027,0.00001059668,0.0001935236,0.04893257,0.003627602,0.00001205238,0.00004641378],"genre_scores_gemma":[0.000009888524,0.8733818,0.09599999,0.00004865824,0.0003563712,0.02720417,0.002881581,0.00006603764,0.00005154455],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9935614,"threshold_uncertainty_score":0.9997666,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2025701648","doi":"10.1038/nprot.2011.319","title":"Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst","year":2011,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Metabolomics and Mass Spectrometry Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1386,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"National Institute for Nanotechnology; University of Alberta","funders":"Canadian Institutes of Health Research","keywords":"Metabolomics; Computer science; Database normalization; Univariate; Normalization (sociology); Upload; Biological data; Protocol (science); Data set; Statistical inference; Inference; Data mining; Computational biology; Bioinformatics; Multivariate statistics; Artificial intelligence; Biology; Machine learning; World Wide Web; Pattern recognition (psychology); Statistics; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.1117310879761089,"gpt":0.3366927524806622,"spread":0.2249616645045533,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002930454,0.0002027697,0.0003725039,0.00007772051,0.00007594925,0.00001693053,0.0004228562,0.0003314933,0.00007251863],"category_scores_gemma":[0.0002631535,0.000152153,0.00007558019,0.0001383734,0.000110956,0.000008717282,0.0004440266,0.0002405948,0.000001236869],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005028228,"about_ca_system_score_gemma":0.00009438246,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000897587,"about_ca_topic_score_gemma":0.00007213769,"domain_scores_codex":[0.9987209,0.0001088258,0.000289117,0.0005601562,0.000122483,0.0001984533],"domain_scores_gemma":[0.9987996,0.00003105847,0.0002014387,0.0007880048,0.0001137638,0.00006608401],"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":[0.0002215493,0.0001435174,0.1012487,0.00002935312,0.0002972931,0.000001839037,0.00001334967,0.000001847639,0.8962971,0.00038408,0.0001335603,0.001227849],"study_design_scores_gemma":[0.003008197,0.0006575353,0.1384862,0.00008191387,0.0004074773,0.000005218074,0.0001458192,0.001083612,0.8120359,0.0008898047,0.04248628,0.000712077],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9796991,0.003137366,0.006177965,0.00002325139,0.00009827205,0.008764973,0.001763149,0.00001945099,0.0003164259],"genre_scores_gemma":[0.985515,0.0001388232,0.01135458,0.000110294,0.0001102101,0.00236402,0.0003815043,0.00001413626,0.0000114064],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08426121,"threshold_uncertainty_score":0.620462,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1566831845","doi":"10.1038/nprot.2015.052","title":"NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data","year":2015,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1015,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"Canadian Institutes of Health Research","keywords":"Computer science; Visualization; Data visualization; Data mining; Visual analytics; Metadata; Graph drawing; Context (archaeology); Web application; Information retrieval; Bioinformatics; Biology; World Wide Web","retraction":null,"screen_n_in":null,"score":{"opus":0.07714031460892924,"gpt":0.3876758930110881,"spread":0.3105355784021588,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009283111,0.0001742011,0.000594244,0.00005363609,0.00005502699,0.00004006734,0.0003449606,0.0003693123,0.00001480797],"category_scores_gemma":[0.0001067908,0.0001296783,0.0002038362,0.0002183848,0.00006919241,0.00000651593,0.000197188,0.000154694,3.608876e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005620962,"about_ca_system_score_gemma":0.0001044493,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004219723,"about_ca_topic_score_gemma":0.00003513193,"domain_scores_codex":[0.9987397,0.00007215699,0.0003898144,0.0003728734,0.0001868592,0.0002385504],"domain_scores_gemma":[0.9986169,0.0000643737,0.0002498396,0.0007288434,0.0001974973,0.0001425345],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.005790407,0.0008790758,0.005014527,0.0007311082,0.1844202,0.00000752362,0.0001223169,0.1737522,0.04433078,0.002609508,0.5707511,0.01159132],"study_design_scores_gemma":[0.004240342,0.001720127,0.0003164134,0.00003115033,0.09123041,0.000004218784,0.00004231312,0.5545475,0.03241027,0.001546353,0.3129073,0.001003616],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.0007728616,0.004268358,0.9600426,0.0001708474,0.00007663051,0.03281658,0.001590686,0.00001638561,0.0002450482],"genre_scores_gemma":[0.4411414,0.00001911297,0.5030744,0.002123724,0.001115724,0.03648498,0.01571848,0.00007916868,0.0002429803],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.4569682,"threshold_uncertainty_score":0.5288127,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1989578357","doi":"10.1038/nprot.2012.064","title":"Whole plant cell wall characterization using solution-state 2D NMR","year":2012,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Polysaccharides and Plant Cell Walls","field":"Agricultural and Biological Sciences","cited_by":708,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"","keywords":"Cell wall; Lignin; Characterization (materials science); Plant cell; Chemistry; Computational biology; Biochemical engineering; Nanotechnology; Materials science; Biochemistry; Biology; Organic chemistry","retraction":null,"screen_n_in":null,"score":{"opus":0.02616370290679302,"gpt":0.2541640960959039,"spread":0.2280003931891109,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002472026,0.0001519249,0.0001440981,0.00001239403,0.0001909568,0.0000828929,0.0001916476,0.0002532737,0.0002199061],"category_scores_gemma":[0.00001100707,0.0000598332,0.00006431397,0.0001732032,0.00001528182,0.0003064779,0.00004903629,0.0003173919,0.0001014003],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003017277,"about_ca_system_score_gemma":0.000009548008,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009571209,"about_ca_topic_score_gemma":0.0000356685,"domain_scores_codex":[0.9989248,0.0000576668,0.0001848647,0.0001913304,0.0002054225,0.0004359495],"domain_scores_gemma":[0.9995761,0.00005013117,0.0001397841,0.00005555248,0.00004008573,0.0001383286],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00003326324,0.00009077354,0.00724876,0.00001686377,0.000003770484,0.000001570558,0.00005864502,0.000001781871,0.9872013,0.00003210488,0.0004906576,0.00482047],"study_design_scores_gemma":[0.000234932,0.0001244261,0.1010581,0.0001068699,0.00001247064,0.00002182122,0.00001353964,0.001027339,0.178251,0.00009463377,0.7186427,0.0004121183],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9759805,0.000120795,0.00003983406,0.000415517,0.0001822961,0.02200067,0.0005442515,0.0001050152,0.000611075],"genre_scores_gemma":[0.9915775,0.000009880517,0.0002276501,0.0008409258,0.0007623456,0.004811205,0.0006973486,0.00000257823,0.001070581],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8089503,"threshold_uncertainty_score":0.2439927,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2181192066","doi":"10.1038/nprot.2015.115","title":"Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange","year":2015,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bacterial biofilms and quorum sensing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":609,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Hospital for Sick Children; University of Toronto; University of Calgary","funders":"National Institute of Diabetes and Digestive and Kidney Diseases; National Heart, Lung, and Blood Institute; National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research","keywords":"Pseudomonas aeruginosa; Genome; Computational biology; Biology; Genetics; Allele; Genome engineering; Genome editing; Gene; Bacteria","retraction":null,"screen_n_in":null,"score":{"opus":0.01316137842300327,"gpt":0.2712835548091294,"spread":0.2581221763861261,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002468712,0.0002082177,0.0001553072,0.00002894582,0.00008641658,0.00005893136,0.000263614,0.0002920126,0.000007504482],"category_scores_gemma":[0.00007673281,0.0001267014,0.00006010928,0.0001166674,0.00004960849,0.000006930384,0.0001453542,0.0003389993,0.00001310212],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001869077,"about_ca_system_score_gemma":0.00009075225,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001088048,"about_ca_topic_score_gemma":0.00002537604,"domain_scores_codex":[0.9989505,0.00004874654,0.0001519615,0.000330569,0.0002238232,0.0002944294],"domain_scores_gemma":[0.99915,0.00001257939,0.00007656868,0.0004795588,0.0001545889,0.0001266608],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0004580206,0.00004508673,0.0002662759,0.00002891066,0.00005800972,0.00001925937,0.0001033906,0.000171944,0.9920976,0.00007265228,0.00409654,0.002582312],"study_design_scores_gemma":[0.001505521,0.0004969954,0.001046889,0.00005408525,0.00001032216,0.0001735565,0.0000240736,0.0001049235,0.1178947,0.000005886996,0.8783803,0.000302747],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8911797,0.002789714,0.002030724,0.001880783,0.0005840876,0.09629536,0.00006274847,0.0001696086,0.005007223],"genre_scores_gemma":[0.9594398,0.00003632726,0.01317603,0.001245651,0.002407536,0.02260713,0.0001369477,0.0001038168,0.0008468083],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8742837,"threshold_uncertainty_score":0.5166734,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2002192590","doi":"10.1038/nprot.2006.430","title":"Preparation of ready-to-use, storable and reconstituted type I collagen from rat tail tendon for tissue engineering applications","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Collagen: Extraction and Characterization","field":"Materials Science","cited_by":579,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université Laval","funders":"","keywords":"Acetic acid; Tissue engineering; Extracellular matrix; Type I collagen; Matrix (chemical analysis); Chemistry; In vivo; Biomedical engineering; Tendon; In vitro; Chromatography; Biochemistry; Anatomy; Biology; Biotechnology","retraction":null,"screen_n_in":null,"score":{"opus":0.01587675122913874,"gpt":0.3207665191945391,"spread":0.3048897679654003,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001260539,0.00009643399,0.0001439975,0.00006485593,0.00008197971,0.0001051467,0.00007855767,0.0001684587,0.00006769694],"category_scores_gemma":[0.00009530867,0.00009597874,0.00001341209,0.0002287707,0.00001472311,0.0002672628,0.00001758822,0.0000521643,0.00001549237],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000423421,"about_ca_system_score_gemma":0.00006421069,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006146506,"about_ca_topic_score_gemma":0.00008469307,"domain_scores_codex":[0.9992868,0.00001935068,0.0002325069,0.0002385872,0.0001129968,0.0001098069],"domain_scores_gemma":[0.999306,0.00007680645,0.000135158,0.0001822536,0.0002586684,0.00004114515],"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":[0.0001582581,0.00003858946,0.0001742089,0.00005140463,0.000002623707,2.158893e-7,0.00003053673,0.0002795895,0.9959826,0.0009585519,0.001847522,0.0004758732],"study_design_scores_gemma":[0.0002574297,0.00006881404,0.001345031,0.00003561089,0.000008237403,0.000001452693,0.000004112868,0.0003170368,0.642467,0.00008296459,0.3553248,0.00008751703],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.6228975,0.0001247078,0.1087369,0.0004125435,0.0007568729,0.2646899,0.0009411639,0.00044791,0.0009925327],"genre_scores_gemma":[0.8249556,0.000003177955,0.04183171,0.000111815,0.0003832039,0.129902,0.0005586291,0.00003598405,0.0022179],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3535157,"threshold_uncertainty_score":0.39139,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2101629470","doi":"10.1038/nprot.2006.288","title":"Silver staining of proteins in polyacrylamide gels","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":572,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Defence Research and Development Canada","funders":"","keywords":"Silver stain; Staining; Polyacrylamide; Stain; Electrophoresis; Chromatography; Polyacrylamide gel electrophoresis; Mass spectrometry; Chemistry; Fixation (population genetics); Molecular biology; Biology; Biochemistry","retraction":null,"screen_n_in":null,"score":{"opus":0.008249985199709202,"gpt":0.3112988602053018,"spread":0.3030488750055926,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001129121,0.000132643,0.00018361,0.00006017993,0.00003707028,0.00001359537,0.0002409062,0.0003403538,0.00009781158],"category_scores_gemma":[0.00003823983,0.0001274271,0.00005550874,0.0002097652,0.000044821,0.00007986314,0.00006084181,0.0006347308,0.000002491036],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007418408,"about_ca_system_score_gemma":0.00005153304,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008255258,"about_ca_topic_score_gemma":0.00002969226,"domain_scores_codex":[0.9990365,0.000008175697,0.0003259324,0.0002411344,0.0001683991,0.0002198598],"domain_scores_gemma":[0.9993333,0.00003005133,0.000179534,0.0003627447,0.00006883054,0.00002556776],"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":[0.00005646035,0.000168166,0.008582104,0.0002071256,0.000003741872,0.000004236789,0.00002667516,0.00006122721,0.9563333,0.03128267,0.0001781144,0.003096133],"study_design_scores_gemma":[0.0004446675,0.00001843432,0.0004547237,0.000212523,0.000001851099,0.000002080302,0.00001290198,0.00006365591,0.9353607,0.03553092,0.02775217,0.000145382],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.4742154,0.0004203763,0.0309498,0.001095092,0.00002396803,0.3026974,0.0002787121,0.001120115,0.1891991],"genre_scores_gemma":[0.7030859,9.340941e-7,0.06643692,0.00004038974,0.0000882579,0.2295619,0.00001690573,0.00002824039,0.000740581],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2288705,"threshold_uncertainty_score":0.5196327,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1992577725","doi":"10.1038/nprot.2006.101","title":"Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Enzyme Structure and Function","field":"Materials Science","cited_by":540,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto; Hospital for Sick Children; Canada Research Chairs","funders":"Canadian Institutes of Health Research; Canada Research Chairs","keywords":"Isotopic labeling; Valine; Isoleucine; Nuclear magnetic resonance spectroscopy; Chemistry; Leucine; Isotope; Macromolecule; Deuterium; Stable isotope labeling by amino acids in cell culture; Mass spectrometry; Biochemistry; Alanine; Amino acid; Chromatography; Proteomics; Stereochemistry; Organic chemistry","retraction":null,"screen_n_in":null,"score":{"opus":0.008210618176446902,"gpt":0.2870842680478667,"spread":0.2788736498714198,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003790897,0.0001755927,0.0002107971,0.0000393415,0.0002371623,0.0001396237,0.0002967397,0.0002165493,0.00005498454],"category_scores_gemma":[0.0000415672,0.0001114782,0.00005396036,0.000184854,0.00005715033,0.0002021926,0.00004112966,0.0003021143,0.00000412543],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003882561,"about_ca_system_score_gemma":0.00007534881,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003949844,"about_ca_topic_score_gemma":0.0002819556,"domain_scores_codex":[0.9986591,0.00008088176,0.0003039813,0.0003247211,0.000365331,0.0002659954],"domain_scores_gemma":[0.9991581,0.00006931741,0.0002200712,0.0003461922,0.0001852507,0.00002107055],"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":[0.000220165,0.0001963874,0.00008547879,0.0000722629,0.00001148503,8.012963e-7,0.00007743207,0.0001756553,0.983857,0.01080772,0.004340947,0.0001546054],"study_design_scores_gemma":[0.00134827,0.001152196,0.0003312073,0.00004175741,0.00003360959,0.000001639909,0.0001451349,0.00006656462,0.977376,0.01401866,0.005336069,0.0001488808],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5624059,0.0005436779,0.08868703,0.0006849939,0.0005382595,0.3455988,0.0001221947,0.0002263249,0.001192857],"genre_scores_gemma":[0.886725,3.917983e-7,0.006264237,0.0000654318,0.000293087,0.1065176,0.00001424477,0.00002086476,0.00009910404],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3243191,"threshold_uncertainty_score":0.454595,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2158442971","doi":"10.1038/nprot.2008.183","title":"Electrical stimulation systems for cardiac tissue engineering","year":2009,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Tissue Engineering and Regenerative Medicine","field":"Medicine","cited_by":536,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto","funders":"National Heart, Lung, and Blood Institute; Natural Sciences and Engineering Research Council of Canada; National Institute of Biomedical Imaging and Bioengineering; University of Toronto; Arthritis Foundation","keywords":"Tissue engineering; Pulsatile flow; Biomedical engineering; Stimulation; Cell culture; Cell; Substrate (aquarium); Functional electrical stimulation; Cell biology; Materials science; Nanotechnology; Biophysics; Computer science; Chemistry; Neuroscience; Biology; Medicine; Cardiology; Biochemistry","retraction":null,"screen_n_in":null,"score":{"opus":0.01246891885275006,"gpt":0.3396462018993281,"spread":0.327177283046578,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001828112,0.0001579964,0.00034862,0.0001158371,0.00003944854,0.00001833903,0.00005007843,0.0002968984,0.000003897582],"category_scores_gemma":[0.0002599099,0.0001193884,0.00006625293,0.0002166476,0.0000070541,0.0000353983,0.000003752626,0.0004486961,0.000004804464],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008282403,"about_ca_system_score_gemma":0.0000384111,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001216084,"about_ca_topic_score_gemma":2.519821e-8,"domain_scores_codex":[0.9991171,0.00001310726,0.0001902642,0.000208225,0.0002321163,0.0002391657],"domain_scores_gemma":[0.9994652,0.00005715527,0.00003601865,0.0001816144,0.0001373822,0.0001225964],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0007079003,0.0004120487,0.00195698,0.001604362,0.0002598252,0.00006891452,0.000266589,0.03248703,0.8113185,0.04179479,0.0446348,0.06448831],"study_design_scores_gemma":[0.002803757,0.002641201,0.01277702,0.0006873932,0.00009023061,0.00004965982,0.000004614514,0.05650936,0.05687258,0.00002971857,0.8672388,0.0002956304],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"protocol","genre_gemma":"empirical","genre_scores_codex":[0.01950967,0.04885668,0.345028,0.004105962,0.002588462,0.5769479,0.00004584689,0.001871816,0.001045747],"genre_scores_gemma":[0.8948274,0.00001139909,0.01506378,0.0001270134,0.00497858,0.0773458,0.0001062533,0.00006625394,0.00747353],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8753178,"threshold_uncertainty_score":0.486852,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1972254777","doi":"10.1038/nprot.2007.14","title":"Quick and easy yeast transformation using the LiAc/SS carrier DNA/PEG method","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Fungal and yeast genetics research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":475,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Manitoba","funders":"","keywords":"Transformation (genetics); Yeast; Saccharomyces cerevisiae; PEG ratio; DNA; Lithium (medication); Chemistry; Cell biology; Materials science; Computer science; Computational biology; Biophysics; Biochemistry; Biology; Gene","retraction":null,"screen_n_in":null,"score":{"opus":0.02153621145864548,"gpt":0.3897585241506193,"spread":0.3682223126919739,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008272793,0.0001287378,0.0000990546,0.00003904459,0.0001495923,0.00005466079,0.0001867645,0.0003633507,0.00001165452],"category_scores_gemma":[0.00006248842,0.00008751854,0.00005747188,0.0001329359,0.00006631604,0.000005522402,0.00007266516,0.000375954,0.000002199977],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001397918,"about_ca_system_score_gemma":0.00007911122,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001274768,"about_ca_topic_score_gemma":0.00004373682,"domain_scores_codex":[0.9989755,0.00009227992,0.0001702748,0.0002321745,0.0002471899,0.0002826419],"domain_scores_gemma":[0.999463,0.00001633694,0.0000461286,0.0002418927,0.0001344714,0.00009819225],"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":[0.0002303854,0.00002308195,0.0005821598,0.00006451305,0.00002429361,0.000002542924,0.0001325831,0.00002454334,0.9866304,0.0002375832,0.0002449928,0.01180296],"study_design_scores_gemma":[0.0004878485,0.0001494271,0.001452489,0.0000279112,0.000008180301,0.00003576104,0.00008469794,0.0003167248,0.7810967,0.0001137763,0.216093,0.0001334265],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7620173,0.002885569,0.09243547,0.001333379,0.000491445,0.1267724,0.0002030003,0.00006160372,0.01379985],"genre_scores_gemma":[0.9795254,0.00002583737,0.009274608,0.0007179341,0.0008170183,0.00812253,0.00004985134,0.00004822878,0.001418576],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2175082,"threshold_uncertainty_score":0.3568902,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2246559112","doi":"10.1038/nprot.2015.124","title":"Next-generation diagnostics and disease-gene discovery with the Exomiser","year":2015,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Genomics and Rare Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":466,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Hospital for Sick Children; University of Toronto","funders":"National Institutes of Health","keywords":"Exome; Sanger sequencing; Computational biology; Exome sequencing; Computer science; Suite; DNA sequencing; Genetics; Biology; Gene; Bioinformatics; Mutation","retraction":null,"screen_n_in":null,"score":{"opus":0.02664112301437988,"gpt":0.2800315199897486,"spread":0.2533903969753687,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009252883,0.0001248448,0.00007346074,0.00001216273,0.00008504673,0.0001498816,0.000126058,0.0001173128,0.000001418872],"category_scores_gemma":[0.0001621107,0.00007194922,0.0000309414,0.00004236803,0.0000663812,0.000009700381,0.00007842723,0.0001130474,0.000001746777],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000007192554,"about_ca_system_score_gemma":0.000200792,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002321974,"about_ca_topic_score_gemma":0.00001695107,"domain_scores_codex":[0.9993766,0.00003827722,0.00007576845,0.000244176,0.0001321577,0.0001330352],"domain_scores_gemma":[0.9993697,0.00001005523,0.0000466558,0.0002820509,0.0001025304,0.0001889986],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004235006,0.0007886608,0.04742483,0.0002178871,0.0003643976,0.0001922552,0.0002999205,0.001007808,0.6073498,0.003241835,0.3275354,0.007342178],"study_design_scores_gemma":[0.004040677,0.001189624,0.01986666,0.00008170625,0.00015797,0.00006983246,0.0001761248,0.0003134058,0.1313711,0.001009773,0.84081,0.0009131156],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9541719,0.006848396,0.0007630067,0.002524687,0.0001133016,0.03508819,0.0001509691,0.00001877135,0.0003208032],"genre_scores_gemma":[0.9780949,0.00007412521,0.0003125699,0.001401598,0.000626786,0.01879681,0.0002221692,0.00002250779,0.0004484704],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5132747,"threshold_uncertainty_score":0.2934004,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2070405344","doi":"10.1038/nprot.2006.263","title":"Flow cytometry and FISH to measure the average length of telomeres (flow FISH)","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Telomeres, Telomerase, and Senescence","field":"Medicine","cited_by":445,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia; BC Cancer Agency","funders":"National Cancer Institute; National Institutes of Health","keywords":"Telomere; Flow cytometry; Peptide nucleic acid; Fish <Actinopterygii>; Biology; Pipette; Nucleic acid; Fluorescence in situ hybridization; Cytometry; Computational biology; DNA; Molecular biology; Genetics; Chromosome; Chemistry; Gene","retraction":null,"screen_n_in":null,"score":{"opus":0.01417504627362209,"gpt":0.2925768734926913,"spread":0.2784018272190693,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005011574,0.000312225,0.0005420879,0.0002392711,0.0001555691,0.00005934938,0.0003014458,0.0004532446,0.0001303691],"category_scores_gemma":[0.0004907511,0.0002053038,0.0001355749,0.0008127214,0.0001475146,0.0001129143,0.00009887555,0.0009814712,0.00001298389],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005588024,"about_ca_system_score_gemma":0.0001272593,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005850251,"about_ca_topic_score_gemma":0.0001847348,"domain_scores_codex":[0.9977618,0.0001007399,0.0004344912,0.000474115,0.0008012524,0.0004275622],"domain_scores_gemma":[0.9984929,0.0001900578,0.0001397553,0.0006716934,0.0003177672,0.0001878582],"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":[0.004803097,0.001827367,0.1864635,0.00352954,0.000472806,0.0003923398,0.002285984,0.000254242,0.07450674,0.001110779,0.3991924,0.3251612],"study_design_scores_gemma":[0.004999529,0.001037611,0.4113331,0.001502204,0.0001216385,0.0002179107,0.0001554357,0.0007231488,0.09499147,0.0004242599,0.4837904,0.0007032616],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5025424,0.002233241,0.001476222,0.03468067,0.0007550961,0.4252727,0.0009279742,0.0008325466,0.03127915],"genre_scores_gemma":[0.9644686,0.00001380621,0.004504524,0.005199486,0.0007442982,0.02320812,0.00003977978,0.00006484232,0.001756555],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4619262,"threshold_uncertainty_score":0.8372047,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2087759495","doi":"10.1038/nprot.2013.002","title":"The mouse excisional wound splinting model, including applications for stem cell transplantation","year":2013,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Wound Healing and Treatments","field":"Medicine","cited_by":441,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta","funders":"National Natural Science Foundation of China; University of Alberta","keywords":"Wound healing; Stem cell; Granulation tissue; Matrigel; Transplantation; Medicine; Regeneration (biology); Angiogenesis; Wound closure; Progenitor cell; Surgery; Biomedical engineering; Biology; Cell biology; Cancer research","retraction":null,"screen_n_in":null,"score":{"opus":0.04735381737145444,"gpt":0.3822005986685074,"spread":0.3348467812970529,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000210047,0.0001140696,0.0001311336,0.0000380836,0.0005108449,0.00007473696,0.00009196781,0.0001985914,0.000006013127],"category_scores_gemma":[0.00001005355,0.00007172314,0.00007196813,0.00008412147,0.00002236802,0.00007812863,0.00001189788,0.0003333754,0.00003092147],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007292048,"about_ca_system_score_gemma":0.00008202773,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000008076954,"about_ca_topic_score_gemma":0.000004328539,"domain_scores_codex":[0.999127,0.00001503839,0.0002227914,0.0002064314,0.0002217896,0.0002069159],"domain_scores_gemma":[0.9992127,0.0002095816,0.00008878022,0.0002134951,0.0001990433,0.00007633868],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.007456118,0.00623825,0.02983045,0.01569741,0.001115805,0.00002844366,0.007373707,0.005597332,0.1973169,0.09796117,0.03971723,0.5916672],"study_design_scores_gemma":[0.04235093,0.002448357,0.01246233,0.002245314,0.001056764,0.0002048642,0.001194098,0.192431,0.2408769,0.09933835,0.403391,0.002000025],"study_design_candidate":"design_other","study_design_consensus":null,"genre_codex":"protocol","genre_gemma":"protocol","genre_scores_codex":[0.1455907,0.000387603,0.0969689,0.004365821,0.00008246368,0.7458565,0.0001088158,0.0003633437,0.006275909],"genre_scores_gemma":[0.4491825,0.000009039305,0.01442405,0.0002933277,0.0001835639,0.5322309,0.00008531594,0.00002832683,0.003562996],"genre_candidate":"protocol","genre_consensus":"protocol","teacher_disagreement_score":0.5896672,"threshold_uncertainty_score":0.3929057,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2068674866","doi":"10.1038/nprot.2012.039","title":"Genome-wide copy number analysis of single cells","year":2012,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":434,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Ontario Institute for Cancer Research","funders":"National Cancer Institute","keywords":"Copy-number variation; Genome; Single cell sequencing; Biology; DNA sequencing; Computational biology; Genomics; Copy number analysis; Sorting; Genetics; DNA; Phenotype; Gene; Computer science; Exome sequencing; Algorithm","retraction":null,"screen_n_in":null,"score":{"opus":0.009892517596263738,"gpt":0.2766138917601147,"spread":0.2667213741638509,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001513548,0.0001096034,0.0001798789,0.00005118382,0.00004008018,0.00001400477,0.0001517082,0.0002666279,0.0002694432],"category_scores_gemma":[0.00002784697,0.00009801325,0.0001542525,0.0002303756,0.00003272211,0.000005448285,0.0000679991,0.0001054098,0.00001813005],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001541558,"about_ca_system_score_gemma":0.00003040108,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006755331,"about_ca_topic_score_gemma":0.0000078157,"domain_scores_codex":[0.9992808,0.00004109402,0.000199929,0.0001515331,0.0001118577,0.0002148139],"domain_scores_gemma":[0.9994034,0.00001180836,0.0001185031,0.0002985212,0.0001030184,0.00006479806],"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":[0.00005111349,0.0002294577,0.3587965,0.00003861331,0.0005084777,3.067165e-7,0.0001335204,0.00008279352,0.6391594,0.000313822,0.0006283756,0.0000576168],"study_design_scores_gemma":[0.0002388641,0.00007826629,0.06736691,0.000005789508,0.0001549592,0.000001822698,0.00004464399,0.000002805285,0.7811234,0.00002754651,0.1508086,0.0001464037],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9805599,0.0001721968,0.0006623387,0.00003656591,0.00007614173,0.009749801,0.0001002394,0.00001146276,0.008631296],"genre_scores_gemma":[0.9918867,0.000002866449,0.001520858,0.0001606825,0.0001683468,0.005161251,0.0001331138,0.00001212281,0.0009540468],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2914296,"threshold_uncertainty_score":0.3996865,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2060756795","doi":"10.1038/nprot.2007.15","title":"Large-scale high-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Fungal and yeast genetics research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":417,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Manitoba","funders":"","keywords":"Transformation (genetics); Yeast; Saccharomyces cerevisiae; Transformation efficiency; Plasmid; Genomic library; PEG ratio; DNA; Protoplast; Computational biology; Molecular biology; Chemistry; Biology; Cell biology; Computer science; Biochemistry; Gene; Base sequence; Agrobacterium","retraction":null,"screen_n_in":null,"score":{"opus":0.01576373665039952,"gpt":0.3712872066783656,"spread":0.355523470027966,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001239379,0.0001664924,0.0001290808,0.00005562549,0.0002360483,0.00005761668,0.0003678445,0.0004648215,0.00003424262],"category_scores_gemma":[0.00006290583,0.0001139548,0.0001060906,0.0002654521,0.00005888279,0.000006724831,0.00009622059,0.0005089683,0.000007660113],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002592578,"about_ca_system_score_gemma":0.0001206262,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001133653,"about_ca_topic_score_gemma":0.00006972023,"domain_scores_codex":[0.9984577,0.0001182433,0.0002423403,0.0003103885,0.000402131,0.0004692557],"domain_scores_gemma":[0.9992157,0.00001718183,0.00006614378,0.0003825752,0.0002085188,0.0001098683],"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":[0.0002120021,0.00009257029,0.0002476672,0.00005442095,0.00002126948,0.000003205929,0.0003280327,0.0001763176,0.9946485,0.0003329044,0.0004521564,0.003430988],"study_design_scores_gemma":[0.0006199608,0.0001736874,0.0007084289,0.00002555068,0.000009326615,0.00001804244,0.0001957751,0.0008776985,0.8299538,0.0001020852,0.1671524,0.0001632696],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.5369569,0.0007897449,0.3764215,0.0007628105,0.0005684894,0.07768299,0.0003009777,0.0000580634,0.006458513],"genre_scores_gemma":[0.9809347,0.000008787918,0.008767819,0.00051676,0.0007964001,0.007667055,0.00008891449,0.0000461894,0.001173317],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4439779,"threshold_uncertainty_score":0.4646941,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3014687364","doi":"10.1038/s41596-020-0313-9","title":"Tutorial: guidance for quantitative confocal microscopy","year":2020,"lang":"en","type":"review","venue":"Nature Protocols","topic":"Cell Image Analysis Techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":401,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"McGill University; University Health Network","funders":"Francis Crick Institute","keywords":"Confocal microscopy; Microscopy; Confocal; Computer science; Computational biology; Nanotechnology; Biology; Optics; Materials science; Physics; Cell biology","retraction":null,"screen_n_in":null,"score":{"opus":0.03443722157121924,"gpt":0.4614982103708785,"spread":0.4270609887996593,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.000315468,0.0004982714,0.001330624,0.00006738518,0.00006457888,0.00009227378,0.0006806114,0.001591872,0.00001045558],"category_scores_gemma":[0.0007938985,0.0004198155,0.0009048046,0.0002080133,0.0000893103,0.00000374926,0.0001914457,0.0006925481,0.00001958045],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004871101,"about_ca_system_score_gemma":0.0004707566,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002156948,"about_ca_topic_score_gemma":0.000004948376,"domain_scores_codex":[0.9979421,0.0001559903,0.0005781846,0.0008657991,0.0001699334,0.000287971],"domain_scores_gemma":[0.9983867,0.000065658,0.0005021468,0.0006538454,0.0002990838,0.00009259852],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003244672,0.0001403254,0.000001707643,0.025956,0.0009832293,0.00001946388,0.00001745345,1.051995e-7,0.02220643,0.001237216,0.4151201,0.5339935],"study_design_scores_gemma":[0.0002639831,0.0004846863,4.568178e-8,0.002664713,0.0002724219,0.000007172058,0.00000143969,0.000001784657,0.03014608,0.00006463335,0.9656693,0.0004237451],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[3.444128e-8,0.8839758,0.005093534,0.00002434072,0.00006138821,0.1100646,0.0001214768,0.00005231326,0.0006064761],"genre_scores_gemma":[1.889751e-7,0.6788015,0.02556848,0.0002448093,0.001053819,0.2927842,0.0007889083,0.0001037271,0.0006544219],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.5505492,"threshold_uncertainty_score":0.9998254,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2071099979","doi":"10.1038/nprot.2007.17","title":"Frozen competent yeast cells that can be transformed with high efficiency using the LiAc/SS carrier DNA/PEG method","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Fungal and yeast genetics research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":390,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Manitoba","funders":"","keywords":"Yeast; PEG ratio; Transformation (genetics); DNA; Molecular biology; Biology; Chemistry; Biochemistry; Gene","retraction":null,"screen_n_in":null,"score":{"opus":0.02276099571247803,"gpt":0.3439219365059161,"spread":0.321160940793438,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007533788,0.0002591438,0.0002088361,0.00005036312,0.0002643529,0.00008656183,0.0005154779,0.0004268173,0.0000331253],"category_scores_gemma":[0.00002462112,0.0001559672,0.0001111475,0.0002385606,0.0001511024,0.000003772899,0.0001074551,0.0006317939,0.000001626831],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004090421,"about_ca_system_score_gemma":0.0002645827,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001198308,"about_ca_topic_score_gemma":0.0003627782,"domain_scores_codex":[0.9980022,0.0001320569,0.0002089903,0.0004674508,0.0005991004,0.0005902537],"domain_scores_gemma":[0.9989908,0.00003077097,0.00008166122,0.0005077801,0.0002042826,0.0001846452],"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":[0.0005257661,0.00008750702,0.0007355788,0.00006161367,0.00006089889,0.0000136265,0.0001419889,0.0002378484,0.9963511,0.0000626441,0.0003777492,0.001343706],"study_design_scores_gemma":[0.000977593,0.000444155,0.0007420075,0.00004947335,0.00002053393,0.00002856758,0.0001290483,0.0000941329,0.9496032,0.00002673916,0.04764541,0.0002391341],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8808972,0.0004781232,0.02181938,0.001102199,0.0004078716,0.09144345,0.0004104237,0.00005004181,0.003391288],"genre_scores_gemma":[0.9832971,0.000008631909,0.007033534,0.0006827252,0.0003987299,0.007093626,0.00006035464,0.00006077856,0.001364504],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1023999,"threshold_uncertainty_score":0.6360157,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2430232674","doi":"10.1038/nprot.2016.071","title":"Electrochemical detection of nucleic acids, proteins, small molecules and cells using a DNA-nanostructure-based universal biosensing platform","year":2016,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Advanced biosensing and bioanalysis techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":389,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Kellogg's (Canada)","funders":"","keywords":"Biosensor; Nucleic acid; DNA; Nanostructure; Nanotechnology; Computational biology; Small molecule; DNA nanotechnology; Chemistry; Biophysics; Biology; Biochemistry; Materials science","retraction":null,"screen_n_in":null,"score":{"opus":0.008101621633010524,"gpt":0.2566430368443015,"spread":0.2485414152112909,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001067582,0.0002230938,0.0002179737,0.00009922666,0.00007587454,0.00001852447,0.0001169077,0.0006056385,5.071167e-7],"category_scores_gemma":[0.00008469402,0.0001562018,0.0001047199,0.0001574358,0.0001730496,0.000007979218,0.00006736006,0.0001974273,1.698305e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004323042,"about_ca_system_score_gemma":0.00007802076,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000354112,"about_ca_topic_score_gemma":0.00001610564,"domain_scores_codex":[0.9989276,0.00004265064,0.0002183688,0.000417398,0.000143203,0.0002507832],"domain_scores_gemma":[0.9992682,0.00001411918,0.0002016426,0.0002835959,0.0001640811,0.00006830716],"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":[0.0004352565,0.00002784679,0.00007605493,0.00004474767,0.00003229371,0.000002430767,0.000003320514,7.382133e-7,0.9947489,0.00001567818,0.000005269947,0.004607458],"study_design_scores_gemma":[0.0007012123,0.000378583,0.00005233335,0.0001801567,0.0000299706,0.0000213811,0.000006465609,0.0001302284,0.9966201,0.0001572614,0.001491993,0.0002302783],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9459139,0.00006610052,0.04449542,0.00007467999,0.00001825256,0.009327201,0.00002051431,0.00005705967,0.00002688226],"genre_scores_gemma":[0.9544568,0.000006894948,0.04502028,0.00009157038,0.00008040728,0.0002933822,0.00001009172,0.00002655232,0.00001403424],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.009033819,"threshold_uncertainty_score":0.6369726,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2409887094","doi":"10.1038/nprot.2016.070","title":"A method for detergent-free isolation of membrane proteins in their local lipid environment","year":2016,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Lipid Membrane Structure and Behavior","field":"Biochemistry, Genetics and Molecular Biology","cited_by":389,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta","funders":"Biotechnology and Biological Sciences Research Council; Medical Research Council; Wellcome Trust","keywords":"Membrane protein; Biochemistry; Membrane; Circular dichroism; Ultracentrifuge; Protein purification; Chemistry; Peripheral membrane protein; Nanodisc; Integral membrane protein; Chromatography; Biology","retraction":null,"screen_n_in":null,"score":{"opus":0.01068277477297891,"gpt":0.2957699031960584,"spread":0.2850871284230795,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002706847,0.0001669901,0.0002002582,0.00004939226,0.00002321005,0.000005336177,0.0002758076,0.0004432752,0.00003460856],"category_scores_gemma":[0.00007630602,0.0001027175,0.0001203416,0.00005094697,0.00004730637,0.000006396254,0.00009833041,0.0001215944,0.00000115328],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000241955,"about_ca_system_score_gemma":0.00005217604,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004262348,"about_ca_topic_score_gemma":0.00003351938,"domain_scores_codex":[0.9989716,0.00007193416,0.000270744,0.0003423631,0.0001301766,0.000213226],"domain_scores_gemma":[0.9992718,0.00002478774,0.0001245009,0.000483906,0.00004671795,0.00004829921],"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":[0.0005126123,0.00007948336,0.0006150769,0.00008938916,0.00001556133,3.223538e-7,0.00002174182,0.000007420891,0.9622256,0.00007291738,0.0001083223,0.0362516],"study_design_scores_gemma":[0.002228898,0.0005099011,0.0007742803,0.00007090368,0.000009918776,0.00000408277,0.000007322749,0.00002164492,0.9377463,0.0002026893,0.05828149,0.0001425371],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1868544,0.0001230284,0.5977121,0.001344301,0.0002328286,0.2129101,0.0004585554,0.00003693442,0.0003277805],"genre_scores_gemma":[0.8020408,0.00001150825,0.07096156,0.0001982087,0.0005336014,0.1257398,0.00005439194,0.0000494731,0.0004107039],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.6151864,"threshold_uncertainty_score":0.4188699,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4210617107","doi":"10.1038/s41596-021-00659-2","title":"Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking","year":2022,"lang":"en","type":"review","venue":"Nature Protocols","topic":"Computational Drug Discovery Methods","field":"Computer Science","cited_by":389,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"Canadian Institutes of Health Research; Michael Smith Health Research BC; Vancouver Coastal Health Research Institute; Fondazione Zegna","keywords":"Virtual screening; Computer science; Workflow; Chemical database; Docking (animal); Drug discovery; Bioinformatics; Database; Biology","retraction":null,"screen_n_in":null,"score":{"opus":0.07732661057771312,"gpt":0.3948962207137753,"spread":0.3175696101360622,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.001350226,0.0005998004,0.001610393,0.0004156485,0.0002186762,0.0004231948,0.002876613,0.0005743895,0.0001128807],"category_scores_gemma":[0.0005650067,0.0004755524,0.0004775326,0.002146966,0.0001197077,0.0007541152,0.001006405,0.002666109,0.000006386153],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001279966,"about_ca_system_score_gemma":0.001137248,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000002076617,"about_ca_topic_score_gemma":9.421124e-7,"domain_scores_codex":[0.9952289,0.0007790488,0.00110408,0.001046945,0.001291223,0.0005497792],"domain_scores_gemma":[0.9958344,0.002111191,0.0009021505,0.0008896672,0.000133325,0.0001292986],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00004422773,0.000121913,0.000001378929,0.002504997,0.0001057561,0.00002940732,0.0001686596,0.001002294,0.000001534584,0.1480833,0.00002463518,0.8479119],"study_design_scores_gemma":[0.0001243568,0.0002812906,6.204226e-7,0.006904732,0.00009947501,0.0001029315,0.00003619826,0.009963805,0.0008209635,0.01256676,0.9683126,0.00078631],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[4.677633e-7,0.2942228,0.6619292,0.0000258919,0.0001332767,0.04303465,0.00003232598,0.0001489969,0.0004723677],"genre_scores_gemma":[0.00007877973,0.102964,0.6366185,0.0002584874,0.000762991,0.2587235,0.0003044108,0.0002331017,0.00005628061],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.9682879,"threshold_uncertainty_score":0.9997696,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2039231543","doi":"10.1038/nprot.2006.273","title":"Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":346,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Canada Research Chairs; University of Toronto","funders":"Canadian Institutes of Health Research; National Science Council","keywords":"Fractionation; Proteome; Differential centrifugation; Proteomics; Cell fractionation; Golgi apparatus; Mass spectrometry; Chemistry; Chromatography; Sample preparation; Endoplasmic reticulum; Centrifugation; Protein subcellular localization prediction; Tandem mass spectrometry; Extraction (chemistry); Protein purification; Cytosol; Biochemistry; Membrane; Enzyme","retraction":null,"screen_n_in":null,"score":{"opus":0.0131235428332883,"gpt":0.3257979094989947,"spread":0.3126743666657064,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001696228,0.0001808471,0.0001625145,0.0001335881,0.0001138564,0.0000958317,0.0001104198,0.0005292034,0.00003692971],"category_scores_gemma":[0.00008876444,0.000191454,0.0000416684,0.0002207584,0.00003164572,0.0002894592,0.00001347837,0.0006359285,0.000001702973],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002047176,"about_ca_system_score_gemma":0.00005044585,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004721406,"about_ca_topic_score_gemma":0.00003430393,"domain_scores_codex":[0.9988929,0.00001276751,0.0002998197,0.0004048643,0.0001692538,0.0002204152],"domain_scores_gemma":[0.9992658,0.00007732448,0.0002215139,0.000271777,0.0001268975,0.00003669807],"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":[0.0001565142,0.0001330198,0.001347517,0.0001830557,0.000002442903,0.000001585387,0.000001932991,0.00008477247,0.9881278,0.009051038,0.00007879698,0.000831479],"study_design_scores_gemma":[0.0008814901,0.00004031284,0.0002619173,0.00009952747,0.000004285223,0.00000310368,0.000002764491,0.001758832,0.9270076,0.02874988,0.04098381,0.0002064589],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.04185538,0.0000337331,0.8626705,0.0003752438,0.000008317478,0.09421336,0.00008012565,0.0002246845,0.0005386959],"genre_scores_gemma":[0.1076072,6.955409e-7,0.5661593,0.00002449293,0.0001105369,0.3254465,0.0001245348,0.00003153926,0.0004951972],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.2965112,"threshold_uncertainty_score":0.7807266,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2050938473","doi":"10.1038/nprot.2006.224","title":"BrdU assay for neurogenesis in rodents","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Neurogenesis and neuroplasticity mechanisms","field":"Neuroscience","cited_by":345,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Hospital for Sick Children; University of Toronto","funders":"Canadian Institutes of Health Research","keywords":"Neurogenesis; Bromodeoxyuridine; Proliferation Marker; Cell biology; Biology; Cell division; Cell growth; Endogeny; Deoxyuridine; Molecular biology; Cell; Neuroscience; Immunology; DNA; Genetics; Biochemistry","retraction":null,"screen_n_in":null,"score":{"opus":0.0296971783391801,"gpt":0.3266320571587147,"spread":0.2969348788195346,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000262673,0.0002449767,0.0002544421,0.0001775802,0.0001285772,0.0001048266,0.0004550468,0.0002496661,0.00002270131],"category_scores_gemma":[0.0007397203,0.0002246653,0.0001258638,0.0004745814,0.00003589098,0.0001472342,0.00008339962,0.0003884484,0.00003743832],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003188398,"about_ca_system_score_gemma":0.00004397482,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000007070885,"about_ca_topic_score_gemma":0.00002427947,"domain_scores_codex":[0.9977526,0.0002230508,0.0003510267,0.0007521153,0.0004324722,0.0004887201],"domain_scores_gemma":[0.9989182,0.0004987874,0.0001285394,0.0003350319,0.00004842319,0.00007097999],"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":[0.0001540416,0.0002880499,0.001183615,0.0000520198,7.574554e-7,0.00006950979,0.000003990004,0.00008180857,0.9853403,0.01127152,0.000896361,0.0006580401],"study_design_scores_gemma":[0.001108123,0.0001633524,0.002381944,0.00003171043,0.000004600032,0.00002801374,6.091867e-7,0.0005186774,0.9626645,0.001445023,0.03144833,0.0002050651],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7505897,0.00003753842,0.003229178,0.0008387395,0.0009687635,0.2404901,0.0001792352,0.0005131902,0.00315359],"genre_scores_gemma":[0.8887812,0.000001459041,0.00044664,0.002163035,0.0002166752,0.1077797,0.000002910972,0.00007172587,0.0005365774],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1381916,"threshold_uncertainty_score":0.9161586,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2015115839","doi":"10.1038/nprot.2009.150","title":"A protocol for islet isolation from mouse pancreas","year":2009,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Pancreatic function and diabetes","field":"Medicine","cited_by":341,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"","keywords":"Islet; Pancreas; Collagenase; Isolation (microbiology); Biology; Computational biology; Diabetes mellitus; Bioinformatics; Endocrinology; Biochemistry; Enzyme","retraction":null,"screen_n_in":null,"score":{"opus":0.03021052200401832,"gpt":0.377546688036134,"spread":0.3473361660321157,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001681408,0.0001871336,0.0003305853,0.00007971247,0.00007550326,0.00004295584,0.00008077256,0.0004062384,0.0002909572],"category_scores_gemma":[0.0005392453,0.0001416365,0.0001308199,0.0001534483,0.00001896706,0.0001146278,0.000009090421,0.0003758463,0.00004593193],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000617437,"about_ca_system_score_gemma":0.0001081703,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006929205,"about_ca_topic_score_gemma":6.807214e-7,"domain_scores_codex":[0.9988725,0.00003303698,0.0002717992,0.0003163515,0.0002614853,0.0002448935],"domain_scores_gemma":[0.9990737,0.0001069879,0.0001226373,0.0003532619,0.0002037179,0.0001396899],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.02044279,0.002387163,0.0205863,0.0009053497,0.0002249521,0.00001599409,0.0002919481,0.000006033255,0.6181925,0.00617862,0.2836908,0.04707756],"study_design_scores_gemma":[0.01680735,0.002266982,0.01327314,0.0005682543,0.000064361,0.000006374323,0.00001561355,0.001056069,0.1979369,0.006481369,0.7612253,0.0002982203],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"protocol","genre_gemma":"protocol","genre_scores_codex":[0.002668258,0.000005210627,0.001477764,0.00142947,0.00002325745,0.986598,0.00003421027,0.0002308361,0.007532985],"genre_scores_gemma":[0.004976748,5.772951e-8,0.01440332,0.004509755,0.000606913,0.9733694,0.0000768414,0.00002045363,0.002036515],"genre_candidate":"protocol","genre_consensus":"protocol","teacher_disagreement_score":0.4775345,"threshold_uncertainty_score":0.5775768,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1982370151","doi":"10.1038/nprot.2009.179","title":"Protocol for solid-phase microextraction method development","year":2010,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Analytical chemistry methods development","field":"Chemistry","cited_by":337,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Waterloo","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Solid-phase microextraction; Sample preparation; Computer science; Protocol (science); Sample (material); Chromatography; Process engineering; Extraction (chemistry); Biochemical engineering; Chemistry; Gas chromatography–mass spectrometry; Mass spectrometry; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.05197868350479831,"gpt":0.510629054238198,"spread":0.4586503707333998,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.001119016,0.0004132035,0.0004049807,0.00006302003,0.0002374165,0.0001151946,0.0005224547,0.001154512,0.00195345],"category_scores_gemma":[0.001005712,0.0003606137,0.0001697704,0.0001678491,0.00005827107,0.0001341017,0.0001114874,0.002006558,0.00003778756],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000181631,"about_ca_system_score_gemma":0.0005470417,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001074651,"about_ca_topic_score_gemma":0.000005103319,"domain_scores_codex":[0.9974938,0.0000312547,0.0007013133,0.0007333172,0.0004610073,0.0005792843],"domain_scores_gemma":[0.9980899,0.0003423062,0.0003338396,0.0005730184,0.0003848764,0.0002760461],"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":[0.0006712007,0.0005819605,0.00008945543,0.001237893,0.00006624112,0.000006351874,0.00005591927,6.069383e-7,0.9307297,0.0003568002,0.0019491,0.06425478],"study_design_scores_gemma":[0.002360116,0.00001919576,0.00001273779,0.00007835108,0.000008100222,0.00001893899,0.000007105466,0.0001440651,0.5191204,0.0005575999,0.4774214,0.0002519248],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"protocol","genre_gemma":"protocol","genre_scores_codex":[0.00008925943,6.165012e-7,0.233686,0.0002076403,0.00005622051,0.7554291,0.00001758245,0.000252035,0.01026149],"genre_scores_gemma":[0.00008275828,7.465702e-9,0.453342,0.00009976837,0.0002687592,0.5439728,0.00002164291,0.00003824354,0.002174036],"genre_candidate":"protocol","genre_consensus":"protocol","teacher_disagreement_score":0.4754723,"threshold_uncertainty_score":0.9998846,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2040368665","doi":"10.1038/nprot.2007.459","title":"Detecting protein–protein interactions by far western blotting","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Biotin and Related Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":336,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta","funders":"Canadian Institutes of Health Research; Kidney Foundation of Canada","keywords":"Blot; Immunoprecipitation; Membrane protein; Förster resonance energy transfer; Lysis; Biology; Protein–protein interaction; Cell biology; Biochemistry; Membrane; Molecular biology; Chemistry; Fluorescence; Gene","retraction":null,"screen_n_in":null,"score":{"opus":0.007835246386365244,"gpt":0.3184240833271773,"spread":0.3105888369408121,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003755967,0.0001969338,0.000141744,0.00004407355,0.0002452372,0.00004175711,0.0001841934,0.0005824715,0.000009520978],"category_scores_gemma":[0.0001892932,0.0001653178,0.00009145016,0.0001297381,0.00005578316,0.000005537714,0.0001369552,0.0008833501,0.00001549584],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002263563,"about_ca_system_score_gemma":0.0000256131,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009297185,"about_ca_topic_score_gemma":0.00006410876,"domain_scores_codex":[0.9988178,0.00004364736,0.0002603722,0.0003704434,0.000150194,0.0003575307],"domain_scores_gemma":[0.9994072,0.00001193252,0.0001443532,0.0002485654,0.0001134676,0.00007445549],"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":[0.00009926857,0.00006338915,0.00120986,0.0000493173,0.00006461872,0.000004112243,0.00004815784,5.913396e-7,0.9863141,0.00002351987,0.0006695831,0.01145354],"study_design_scores_gemma":[0.0003677391,0.0001514832,0.0002496755,0.0001267043,0.000005329819,0.00001381666,0.00004222655,0.00000205214,0.6965802,0.00002130225,0.3022751,0.0001643901],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8161086,0.003028129,0.01186531,0.001371544,0.000415144,0.1465648,0.00003864192,0.0003022867,0.02030555],"genre_scores_gemma":[0.973186,0.000003668491,0.002018134,0.0003766051,0.0004438866,0.01836973,0.00002109267,0.00004226709,0.00553861],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3016055,"threshold_uncertainty_score":0.6741466,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2041686750","doi":"10.1038/nprot.2011.382","title":"Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates","year":2011,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Advanced Proteomics Techniques and Applications","field":"Chemistry","cited_by":327,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"","keywords":"Proteome; Isotopic labeling; Chemistry; Biochemistry; Protease; Peptide; Isobaric labeling; Stable isotope labeling by amino acids in cell culture; Amine gas treating; Amino acid; Label-free quantification; Lysine; Quantitative proteomics; Proteomics; Enzyme","retraction":null,"screen_n_in":null,"score":{"opus":0.03292652992043294,"gpt":0.3334002278752797,"spread":0.3004736979548468,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001930632,0.0001727036,0.0002308982,0.0000318771,0.0001474398,0.00003343822,0.00024297,0.0001975801,0.00001914538],"category_scores_gemma":[0.0000495963,0.0001214784,0.0000427068,0.00008648096,0.0001846157,0.0001399565,0.0001201093,0.0006367582,5.172024e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001495747,"about_ca_system_score_gemma":0.00001600367,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002636959,"about_ca_topic_score_gemma":0.000003924342,"domain_scores_codex":[0.9990613,0.00001754128,0.000307661,0.0002874551,0.0001357992,0.0001901858],"domain_scores_gemma":[0.9993096,0.00005980177,0.000251129,0.0002751901,0.00006237843,0.00004191653],"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":[0.000361909,0.0001180639,0.02867573,0.001616741,0.00005279394,0.000005823074,0.0008774122,1.096863e-7,0.9503794,0.007264378,0.00002753,0.01062008],"study_design_scores_gemma":[0.001594792,0.00003290505,0.001321305,0.0005860607,0.00003099939,0.00005635762,0.0001125822,0.0001974512,0.9797912,0.01557489,0.0004632083,0.0002382619],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9610947,0.001276972,0.0006907642,0.0001184507,0.00001594352,0.03602222,0.00003144206,0.0001085088,0.0006410312],"genre_scores_gemma":[0.9314566,0.00002290078,0.02133702,0.00003413626,0.00003188987,0.04683723,0.00000748722,0.00001984224,0.0002528691],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02963804,"threshold_uncertainty_score":0.4953744,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3033785808","doi":"10.1038/s41596-020-0327-3","title":"Analysis of task-based functional MRI data preprocessed with fMRIPrep","year":2020,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Functional Brain Connectivity Studies","field":"Neuroscience","cited_by":322,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"McGill University; Montreal Neurological Institute and Hospital","funders":"National Institute of Biomedical Imaging and Bioengineering; National Institute of Mental Health","keywords":"Computer science; Preprocessor; Functional magnetic resonance imaging; Workflow; Software; Artificial intelligence; Identification (biology); Pattern recognition (psychology); Protocol (science); Data mining; Task (project management); Machine learning; Neuroscience; Database; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.08955149778786851,"gpt":0.3371414683119001,"spread":0.2475899705240315,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002615055,0.0001933573,0.0003785785,0.0001677004,0.0001362602,0.00004254627,0.0006635227,0.0001408553,0.0001572073],"category_scores_gemma":[0.008194203,0.0001495218,0.00008960268,0.002593593,0.0001563345,0.00030842,0.0002506154,0.000489573,0.00001401789],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002700261,"about_ca_system_score_gemma":0.0002393707,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004708652,"about_ca_topic_score_gemma":0.00002772656,"domain_scores_codex":[0.9974937,0.0001151531,0.0002441973,0.001119049,0.0008329783,0.0001948993],"domain_scores_gemma":[0.9966704,0.001915679,0.000234901,0.000867357,0.0002230672,0.00008865516],"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":[0.01690733,0.002254999,0.1870308,0.002133177,0.003311515,0.0001095015,0.0008186602,0.1014781,0.5572754,0.003982826,0.12167,0.003027689],"study_design_scores_gemma":[0.005073285,0.001693056,0.06804815,0.0001883874,0.001236687,0.000008150923,0.0000723407,0.131053,0.6058028,0.0003276877,0.1854865,0.001009975],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"protocol","genre_gemma":"empirical","genre_scores_codex":[0.06695013,0.0003411259,0.167536,0.2149501,0.0006471155,0.516402,0.007631107,0.002893713,0.02264869],"genre_scores_gemma":[0.9567624,3.632075e-7,0.001050647,0.01212525,0.0001255525,0.02976153,0.00007984466,0.000023375,0.00007099043],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8898123,"threshold_uncertainty_score":0.9809818,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2975652314","doi":"10.1038/s41596-019-0213-z","title":"Generation of blood vessel organoids from human pluripotent stem cells","year":2019,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Angiogenesis and VEGF in Cancer","field":"Biochemistry, Genetics and Molecular Biology","cited_by":312,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"","keywords":"Matrigel; Organoid; Induced pluripotent stem cell; Cell biology; Mural cell; Mesoderm; Biology; Vasculogenesis; Stem cell; Anatomy; Blood vessel; Endothelial stem cell; Embryonic stem cell; Angiogenesis; Progenitor cell; In vitro; Cancer research; Endocrinology","retraction":null,"screen_n_in":null,"score":{"opus":0.01905460131110429,"gpt":0.2936245879442643,"spread":0.27456998663316,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000093525,0.0001316776,0.0001577157,0.00002188624,0.0000369554,0.00001693084,0.0001913954,0.0004145177,0.0001187738],"category_scores_gemma":[0.000003297261,0.000113708,0.00009993344,0.00005841317,0.00002195686,0.000003393434,0.00006710634,0.0001257129,0.00001496531],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008346942,"about_ca_system_score_gemma":0.00005713095,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001226636,"about_ca_topic_score_gemma":0.000007403145,"domain_scores_codex":[0.9991382,0.00003713189,0.0002093319,0.0003186624,0.0001619035,0.0001347698],"domain_scores_gemma":[0.999307,0.000003874819,0.0001336394,0.0003921035,0.0001239425,0.00003942081],"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":[0.00003184258,0.00008253039,0.003461758,0.00003847076,0.00007049404,6.207012e-7,0.00001603277,0.00002520324,0.9930653,0.0001159908,0.002573528,0.0005182434],"study_design_scores_gemma":[0.000714547,0.0002772836,0.0009823783,0.00003417848,0.00002349872,7.224469e-7,0.000008132007,0.00001403756,0.9461051,0.00002228441,0.05168309,0.0001347137],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9818483,0.0007592358,0.0001277655,0.00003075917,0.0001322802,0.01656346,0.00006190142,0.000009720771,0.0004665639],"genre_scores_gemma":[0.9902279,0.00001321448,0.0005394701,0.0002078163,0.0005789035,0.007141952,0.0001098752,0.00002661226,0.001154271],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04910956,"threshold_uncertainty_score":0.4636878,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2091655993","doi":"10.1038/nprot.2011.407","title":"Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control","year":2011,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Advanced Fluorescence Microscopy Techniques","field":"Biochemistry, Genetics and Molecular Biology","cited_by":306,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"McGill University","funders":"McGill University","keywords":"Microscope; Confocal; Optics; Lens (geology); Confocal microscopy; Point spread function; 4Pi microscope; Laser; Materials science; Optical microscope; Resolution (logic); Laser scanning; Microscopy; Image quality; Computer science; Sample (material); Confocal laser scanning microscope; Fluorescence microscope; Artificial intelligence; Fluorescence; Physics; Scanning electron microscope; Chemistry; Chromatography; Image (mathematics); Multiphoton fluorescence microscope","retraction":null,"screen_n_in":null,"score":{"opus":0.0319930650342615,"gpt":0.3323045245922448,"spread":0.3003114595579833,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003868864,0.0001735363,0.0001783046,0.00004364808,0.0001040934,0.00003199793,0.000114066,0.0003450128,0.000005151423],"category_scores_gemma":[0.0004330763,0.0001615266,0.00003477998,0.00005202288,0.0001130387,0.00001141128,0.0001514166,0.0003174766,0.000001867621],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002144448,"about_ca_system_score_gemma":0.00002749187,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002417928,"about_ca_topic_score_gemma":0.00005314503,"domain_scores_codex":[0.9989347,0.00009236565,0.000231345,0.0004271265,0.00008568314,0.0002287188],"domain_scores_gemma":[0.9993754,0.00001828358,0.00009055996,0.0002730171,0.000135918,0.0001068342],"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":[0.0006452655,0.00002696498,0.008248309,0.00004530089,0.00001334616,0.000001603329,0.0001045477,4.055464e-7,0.9864093,0.00004322745,0.0002852405,0.004176511],"study_design_scores_gemma":[0.0006770511,0.0005590549,0.007971271,0.0002259552,0.000009859325,0.00002889374,0.00004068721,0.00001912639,0.9805613,0.0001046746,0.009571849,0.000230235],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4383652,0.001239115,0.4658448,0.000398102,0.0001783295,0.09125884,0.0002238393,0.0002457238,0.002246083],"genre_scores_gemma":[0.9273443,0.000005679009,0.05734265,0.0006231081,0.00007519684,0.01449353,0.00001330886,0.00002622561,0.00007598657],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.4889792,"threshold_uncertainty_score":0.6586863,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2031743844","doi":"10.1038/nprot.2010.71","title":"Microtiter susceptibility testing of microbes growing on peg lids: a miniaturized biofilm model for high-throughput screening","year":2010,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bacterial biofilms and quorum sensing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":285,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Calgary","funders":"","keywords":"Microtiter plate; Biofilm; PEG ratio; High-throughput screening; Sonication; Microbiology; Chemistry; Throughput; Antimicrobial; Chromatography; Biology; Bacteria; Biochemistry; Computer science","retraction":null,"screen_n_in":null,"score":{"opus":0.02028803969628937,"gpt":0.3012764629289494,"spread":0.28098842323266,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003454424,0.0002863684,0.0003293698,0.00005960414,0.000159127,0.00004643049,0.0002564152,0.0008549236,0.000005141848],"category_scores_gemma":[0.0005985722,0.0002503145,0.0001853582,0.0001147926,0.0001244051,0.00001524771,0.000131493,0.0005536674,0.000001186589],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000009030173,"about_ca_system_score_gemma":0.0001077698,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001998922,"about_ca_topic_score_gemma":0.00003388563,"domain_scores_codex":[0.9984217,0.00004424265,0.0003920107,0.0006192396,0.0001361255,0.0003867235],"domain_scores_gemma":[0.9987583,0.00006818283,0.000238561,0.0005389909,0.0003188127,0.00007721646],"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":[0.0007204174,0.0001059641,0.0006336957,0.0001268182,0.00003300376,0.000001038966,0.00003835326,0.0000213237,0.9952952,0.00009455562,0.0006359178,0.002293685],"study_design_scores_gemma":[0.001549898,0.0004634275,0.0007438675,0.0001584249,0.0000151619,0.00001339185,0.000007854105,0.0006339155,0.9904708,0.0000581206,0.005586348,0.000298818],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9764447,0.00002285838,0.0009122482,0.0001806115,0.0001755773,0.02200023,0.0001520434,0.00003150459,0.00008028197],"genre_scores_gemma":[0.7327133,9.896153e-7,0.2623792,0.0004667215,0.0005130285,0.003657304,0.0001166662,0.00004539721,0.0001072841],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.261467,"threshold_uncertainty_score":0.9999949,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2010560388","doi":"10.1038/nprot.2007.160","title":"Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Chemical Synthesis and Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":279,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"","keywords":"Peptide; Cellulose; Combinatorial chemistry; Cleavage (geology); Amino acid; Chemistry; Membrane; Peptide synthesis; Biochemistry; Materials science","retraction":null,"screen_n_in":null,"score":{"opus":0.00903648897586372,"gpt":0.315293399113369,"spread":0.3062569101375053,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001237806,0.0001911681,0.0004427686,0.00009011591,0.00003320033,0.00001206069,0.0001325376,0.0003819309,0.00003006315],"category_scores_gemma":[0.0009003158,0.0001597959,0.0001468449,0.000124925,0.00007005816,0.000003506134,0.00006521312,0.0001505535,8.426714e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001667287,"about_ca_system_score_gemma":0.00002949394,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001496159,"about_ca_topic_score_gemma":0.00005576397,"domain_scores_codex":[0.9986624,0.00007440747,0.0003890348,0.0004099132,0.0001746922,0.0002895827],"domain_scores_gemma":[0.9988785,0.0004830635,0.0002232284,0.0002414237,0.00008336629,0.00009042558],"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":[0.001050494,0.0004486991,0.002569215,0.0003694224,0.00007356615,0.000002536555,0.00004679796,0.00006279647,0.9889553,0.0001687358,0.0004938226,0.005758579],"study_design_scores_gemma":[0.0006872578,0.0001615936,0.0009989509,0.0002600768,0.00005777479,0.000002984178,0.0000658951,0.0005674446,0.992231,0.00003359254,0.004750201,0.0001832027],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9609498,0.0002093608,0.006150739,0.0001677301,0.0000116317,0.02996212,0.000355937,0.00001302438,0.002179643],"genre_scores_gemma":[0.9783087,0.00001610136,0.01248396,0.00006491008,0.00003995267,0.008863258,0.00002681257,0.0000241012,0.0001721792],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02109886,"threshold_uncertainty_score":0.6516289,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1983114104","doi":"10.1038/nprot.2006.485","title":"Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Parasitic Infections and Diagnostics","field":"Immunology and Microbiology","cited_by":273,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Saskatchewan","funders":"","keywords":"Single-strand conformation polymorphism; Amplicon; Point mutation; Genetics; Biology; Computational biology; DNA sequencing; genomic DNA; Sequence analysis; Polymerase chain reaction; DNA; Mutation; Gene; Molecular biology","retraction":null,"screen_n_in":null,"score":{"opus":0.01086760944487278,"gpt":0.2855510263686026,"spread":0.2746834169237298,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001568281,0.00007564398,0.0001546324,0.0001318097,0.0001379635,0.00001217946,0.00008305778,0.0003006623,0.00009217102],"category_scores_gemma":[0.0001209957,0.00005252787,0.0001119434,0.0002807287,0.00005718673,0.0000456403,0.000007734086,0.0001460947,0.000008935574],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001936323,"about_ca_system_score_gemma":0.0000282723,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008472549,"about_ca_topic_score_gemma":0.00003741511,"domain_scores_codex":[0.999465,0.00003792884,0.0002530297,0.0000912826,0.00002991322,0.0001227956],"domain_scores_gemma":[0.9990697,0.0004267161,0.0001686226,0.0001597904,0.0001704492,0.000004738086],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.001240936,0.001625127,0.05748562,0.0002248715,0.005026219,0.000001527115,0.0009122936,0.01266441,0.7800666,0.09282023,0.01585834,0.03207382],"study_design_scores_gemma":[0.003147013,0.0003650727,0.7739286,0.0000371186,0.001888817,0.00001391513,0.00002647299,0.001714989,0.1152219,0.002048997,0.1013883,0.0002188912],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.2224459,0.00327397,0.5438116,0.001082322,0.001382185,0.2171262,0.001179352,0.000211644,0.009486767],"genre_scores_gemma":[0.9807488,0.000001585269,0.0005371047,0.00008386703,0.00004448637,0.01822949,0.0001733375,0.000004655973,0.0001766738],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.7583029,"threshold_uncertainty_score":0.2318983,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2038172553","doi":"10.1038/nprot.2008.40","title":"Cardiac tissue engineering using perfusion bioreactor systems","year":2008,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Tissue Engineering and Regenerative Medicine","field":"Medicine","cited_by":272,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto","funders":"National Institute of Biomedical Imaging and Bioengineering; National Heart, Lung, and Blood Institute; National Institutes of Health","keywords":"Tissue engineering; Bioreactor; Biomedical engineering; Cell culture; Perfusion; Scaffold; Materials science; Biochemical engineering; Chemistry; Cell biology; Biology; Medicine; Cardiology; Engineering","retraction":null,"screen_n_in":null,"score":{"opus":0.02730336249502219,"gpt":0.3234197392152813,"spread":0.2961163767202591,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001527334,0.0002323908,0.0004634418,0.0001641805,0.00009476823,0.00001210551,0.00007422108,0.0003714644,0.00002244819],"category_scores_gemma":[0.000141519,0.0001698662,0.00007730474,0.0002804765,0.00003930541,0.00005359587,0.00002659295,0.0007657575,0.00001813936],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001196567,"about_ca_system_score_gemma":0.00008773934,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002601078,"about_ca_topic_score_gemma":9.635779e-8,"domain_scores_codex":[0.9988018,0.00002567988,0.0002288036,0.0002696869,0.0003903775,0.0002836506],"domain_scores_gemma":[0.9992763,0.00003020776,0.00005254571,0.000308703,0.0001358582,0.0001964116],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00004408045,0.00006460013,0.003239592,0.0004840534,0.00005090572,0.0002361608,0.0002312353,0.0008677376,0.9923867,0.000282306,0.001601591,0.0005110459],"study_design_scores_gemma":[0.001804958,0.0005599447,0.008069946,0.001982926,0.00007681087,0.001063454,0.00003606699,0.008174608,0.2625394,5.758833e-7,0.7152681,0.0004231702],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8056421,0.02727952,0.01029212,0.0005167469,0.003435923,0.1510801,0.00003695042,0.001078359,0.0006382483],"genre_scores_gemma":[0.9575979,0.00003368318,0.01061401,0.00003876691,0.004335391,0.02086088,0.00004028778,0.0001217586,0.006357391],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7298473,"threshold_uncertainty_score":0.6926943,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W1971557848","doi":"10.1038/nprot.2007.294","title":"Detergent resistance as a tool in membrane research","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Lipid Membrane Structure and Behavior","field":"Biochemistry, Genetics and Molecular Biology","cited_by":272,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"Natural Sciences and Engineering Research Council of Canada; Deutsche Forschungsgemeinschaft","keywords":"Lipid raft; Raft; Membrane; Computational biology; Chemistry; Biology; Biophysics; Cell biology; Computer science; Biochemistry; Polymer","retraction":null,"screen_n_in":null,"score":{"opus":0.02434389924782985,"gpt":0.4022946295167176,"spread":0.3779507302688878,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001354925,0.0001555387,0.0001504075,0.0001285479,0.00007651389,0.00003147522,0.0003364854,0.0006020603,0.00005960446],"category_scores_gemma":[0.0002979819,0.0001330476,0.00007128622,0.0003369531,0.0000729774,0.000005219059,0.0001113889,0.0007811977,0.00002242869],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004005045,"about_ca_system_score_gemma":0.0001387046,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001028179,"about_ca_topic_score_gemma":0.0006354339,"domain_scores_codex":[0.9982292,0.00009524822,0.0002735288,0.0004608682,0.0004236308,0.0005175134],"domain_scores_gemma":[0.9991663,0.00002648907,0.00004773535,0.0005045165,0.0001816343,0.00007339271],"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":[0.0008048781,0.00007584601,0.002293509,0.00007094723,0.000006898494,0.00004864464,0.00003749472,6.176896e-7,0.9926658,0.0005281611,0.001272127,0.002195042],"study_design_scores_gemma":[0.0006402566,0.0001341872,0.004064423,0.00005255518,0.000001961625,0.00001039389,0.00001715474,1.518263e-7,0.7105914,0.0001659134,0.2841917,0.0001299188],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9497743,0.0001543047,0.00002940521,0.0002308913,0.0001447091,0.03907071,0.000008141996,0.00002028679,0.0105672],"genre_scores_gemma":[0.9732419,0.00000864998,0.0009992553,0.0004166988,0.0005960754,0.02002901,0.00002782998,0.0000296715,0.004650945],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2829195,"threshold_uncertainty_score":0.5425525,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3157420610","doi":"10.1038/s41596-021-00515-3","title":"Microtiter plate assays to assess antibiofilm activity against bacteria","year":2021,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bacterial biofilms and quorum sensing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":267,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of British Columbia","funders":"Canadian Institutes of Health Research; Government of Canada","keywords":"Biofilm; Microtiter plate; Crystal violet; Microbiology; Plate reader; Tetrazolium chloride; Formazan; Bacteria; Resazurin; Chemistry; Biology; Biochemistry; Chromatography; Medicine","retraction":null,"screen_n_in":null,"score":{"opus":0.02103228576030133,"gpt":0.3153547028852563,"spread":0.294322417124955,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001546561,0.0002513039,0.000250743,0.00003843752,0.000126662,0.0001324317,0.0001869114,0.0006990776,0.00003662515],"category_scores_gemma":[0.0001329653,0.0002364909,0.0001329982,0.0001700437,0.00003466574,0.00001085064,0.0002613355,0.0003876786,0.00003819957],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002219532,"about_ca_system_score_gemma":0.0001758516,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003195477,"about_ca_topic_score_gemma":0.00002081381,"domain_scores_codex":[0.9985414,0.0001214486,0.0001901259,0.0006078705,0.0001530159,0.0003860984],"domain_scores_gemma":[0.9989687,0.00001083037,0.00008998068,0.0005471138,0.0002269805,0.0001564096],"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":[0.0002274751,0.00008836166,0.001068445,0.00003598592,0.00004038701,0.00004887134,0.00001179306,0.000001846424,0.9896504,0.00001474934,0.005355328,0.003456392],"study_design_scores_gemma":[0.0003822428,0.0000948874,0.007102294,0.00005363882,0.00000339546,0.00004251236,0.000002803032,0.000002686057,0.7126676,0.000001622176,0.2794133,0.0002329225],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9847494,0.00003392897,0.00008955531,0.0004491979,0.0003376003,0.0124515,0.0001171565,0.00003171589,0.001739901],"genre_scores_gemma":[0.9755186,0.00002102168,0.01428446,0.003619665,0.001112798,0.003832277,0.0003556394,0.00007533736,0.001180225],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2769827,"threshold_uncertainty_score":0.9643819,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W3165190053","doi":"10.1038/s41596-021-00534-0","title":"Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods","year":2021,"lang":"en","type":"review","venue":"Nature Protocols","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":240,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Lunenfeld-Tanenbaum Research Institute; Toronto General Hospital; University of Toronto","funders":"","keywords":"Workflow; Computer science; Annotation; Software; Variety (cybernetics); World Wide Web; Database; Artificial intelligence; Programming language","retraction":null,"screen_n_in":null,"score":{"opus":0.1765710417088984,"gpt":0.5010547193063899,"spread":0.3244836775974915,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.0009629199,0.0008008905,0.00173124,0.0001326834,0.0001954443,0.0002142954,0.0004189682,0.002378302,0.000005436574],"category_scores_gemma":[0.0006230632,0.0007081167,0.0007493676,0.0002441471,0.00008485384,0.00001007898,0.0001051217,0.0007554281,7.061599e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007055941,"about_ca_system_score_gemma":0.0005575739,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009723528,"about_ca_topic_score_gemma":0.000008056042,"domain_scores_codex":[0.9964542,0.0005071957,0.001154009,0.001125017,0.0002185613,0.0005409654],"domain_scores_gemma":[0.9979842,0.0001305267,0.0005150114,0.000540002,0.0006797644,0.000150477],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001427483,0.0002651023,0.000004225011,0.03194045,0.0004349538,0.00001399449,0.00005286828,0.0000122543,0.2052877,0.00005150313,0.008462492,0.7533318],"study_design_scores_gemma":[0.001117749,0.0002897992,1.032429e-7,0.005885354,0.0005292174,0.00007853815,0.00001395859,0.0003354922,0.01891889,0.00002534691,0.9720417,0.0007637967],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.00002240222,0.9387968,0.007908394,0.00002146554,0.0009359722,0.05171213,0.000385987,0.0001277517,0.00008908448],"genre_scores_gemma":[0.000002671877,0.4782961,0.4670735,0.0003919252,0.003461779,0.04786795,0.002015145,0.0003816012,0.000509338],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9635792,"threshold_uncertainty_score":0.999537,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2060528855","doi":"10.1038/nprot.2006.422","title":"Isolation of skin-derived precursors (SKPs) and differentiation and enrichment of their Schwann cell progeny","year":2006,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Nerve injury and regeneration","field":"Neuroscience","cited_by":222,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Hospital for Sick Children; SickKids Foundation; University of Toronto","funders":"","keywords":"Cell biology; Schwann cell; Biology; Neuregulin; Stem cell; Cellular differentiation; Genetics; Signal transduction; Gene","retraction":null,"screen_n_in":null,"score":{"opus":0.01127119064441081,"gpt":0.268714956292307,"spread":0.2574437656478962,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001114175,0.0001077499,0.0001394717,0.00006882707,0.00006908918,0.00002576865,0.00006707975,0.0001655881,0.00000486387],"category_scores_gemma":[0.0000304197,0.00007965606,0.00002867236,0.0001312653,0.00007236569,0.0001566156,0.00003316556,0.0001470887,2.835427e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001004865,"about_ca_system_score_gemma":0.00001877406,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004440727,"about_ca_topic_score_gemma":0.000004222417,"domain_scores_codex":[0.9991498,0.0001078165,0.0002342837,0.0002327838,0.0001788976,0.00009642587],"domain_scores_gemma":[0.9994867,0.00004941698,0.0002541479,0.0001218826,0.0000656706,0.00002214359],"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":[0.00008408567,0.0001416976,0.003501223,0.0001765445,0.00000188442,1.965919e-7,0.0001417102,0.00001351972,0.9921265,0.002721476,0.00002376045,0.00106743],"study_design_scores_gemma":[0.0005404975,0.0001984786,0.02217781,0.00005342522,0.000006728385,0.000001459074,0.000008048746,0.0006097695,0.9746557,0.001486856,0.0001832696,0.00007789802],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9723448,0.00009950404,0.0005998267,0.00005394633,0.00003644457,0.02645687,0.0000184899,0.00001790339,0.0003722452],"genre_scores_gemma":[0.9924187,0.000004478536,0.0005862918,0.00001936807,0.0000486061,0.006821881,0.000007143068,0.000008081967,0.00008545412],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02007392,"threshold_uncertainty_score":0.324828,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2060481943","doi":"10.1038/nprot.2007.427","title":"Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Fungal and yeast genetics research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":220,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Toronto","funders":"","keywords":"Biology; Saccharomyces cerevisiae; Mutant; Gene; Genetics; Computational biology; Genome; DNA microarray; Gene expression","retraction":null,"screen_n_in":null,"score":{"opus":0.01084029872755406,"gpt":0.3451079043860464,"spread":0.3342676056584924,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006926906,0.0001808913,0.0003128714,0.0003399627,0.00004258829,0.0000249773,0.0003650256,0.0004952001,0.00006095321],"category_scores_gemma":[0.0001989418,0.0001514644,0.0001861544,0.0009286568,0.00006000435,0.000004421171,0.0001245095,0.0003506085,0.000004813619],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002784029,"about_ca_system_score_gemma":0.00007616716,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001818106,"about_ca_topic_score_gemma":0.0002556815,"domain_scores_codex":[0.9983301,0.00009250811,0.0004061483,0.0004264679,0.000374226,0.0003705454],"domain_scores_gemma":[0.9991148,0.00002660711,0.0001326588,0.0003839477,0.0002372243,0.0001047402],"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":[0.0003685479,0.0001095875,0.05853469,0.00005832165,0.000268451,0.000008569073,0.00004229538,0.0002494047,0.9390333,0.00001811239,0.00006187549,0.001246818],"study_design_scores_gemma":[0.0005856113,0.0001778954,0.2245017,0.00002617132,0.00005609343,0.000001983677,0.00002777461,0.00006346149,0.7668698,0.00004506636,0.007480844,0.0001635442],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9820389,0.001061202,0.0005339512,0.00008298407,0.00002122936,0.01536728,0.00005499572,0.000009589755,0.0008298798],"genre_scores_gemma":[0.9945168,0.00005673499,0.001011866,0.000130644,0.0001142637,0.00375451,0.0001867283,0.00001844813,0.0002099376],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1721635,"threshold_uncertainty_score":0.6176539,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W2086959309","doi":"10.1038/nprot.2007.151","title":"Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries","year":2007,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Monoclonal and Polyclonal Antibodies Research","field":"Medicine","cited_by":211,"is_retracted":false,"has_abstract":false,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Canada Research Chairs; University of Toronto; University of New Brunswick","funders":"","keywords":"Peptide; Computational biology; Phage display; Peptide library; Fusion protein; Cloning (programming); Peptide sequence; Biology; Chemistry; Computer science; Biochemistry; Gene; Recombinant DNA; Programming language","retraction":null,"screen_n_in":null,"score":{"opus":0.0714665355827465,"gpt":0.3908065595552885,"spread":0.319340023972542,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006433598,0.0002990749,0.0004512957,0.0001967804,0.0002895602,0.00015788,0.000242444,0.0004679848,0.0004783697],"category_scores_gemma":[0.0004445501,0.0002366481,0.0002639632,0.000258173,0.0001513923,0.0003479733,0.0001096347,0.001049062,0.0001251728],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007531616,"about_ca_system_score_gemma":0.0001154196,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001072,"about_ca_topic_score_gemma":0.00008860313,"domain_scores_codex":[0.997567,0.00005730931,0.0004977231,0.0005627651,0.0006968185,0.0006183645],"domain_scores_gemma":[0.9983512,0.0005454437,0.0001631512,0.0003205424,0.0003529083,0.0002667863],"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":[0.04665074,0.002060348,0.08042728,0.005589384,0.001025432,0.0007624663,0.001759366,0.000002666212,0.5188807,0.01074697,0.1260744,0.2060203],"study_design_scores_gemma":[0.003489049,0.0006493329,0.1213808,0.001408541,0.00007777067,0.00004781448,0.0002979702,0.0001827953,0.6569502,0.02513068,0.1898889,0.0004961608],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.737637,0.001232042,0.01120973,0.002718967,0.0004248974,0.2256319,0.001496321,0.0004864279,0.01916272],"genre_scores_gemma":[0.4635553,0.00008049508,0.3118301,0.003002193,0.01026775,0.1776886,0.004860983,0.0002968296,0.02841782],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3006204,"threshold_uncertainty_score":0.9650229,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null}]}