{"meta":{"query_hash":"86fa0a3895a8","filters":{"venue":"Microbial Genomics"},"cohort_total":128,"direct_labels_cover":1,"predictions_cover":128,"exported":128,"export_cap":100000,"truncated":false,"label_status":"direct model label, unvalidated","prediction_status":"machine_predicted_unvalidated (Codex and Gemma teacher distillation)","score_status":"score_only:v0-immature-baseline","snapshot":{"source":"OpenAlex, pinned release, all 482 partitions","release":"2026-06-24","frame_built":"2026-07-12"},"permalink":"https://metacan.xera.ac/q/86fa0a3895a8","api":"https://metacan.xera.ac/api/v1/cohort?venue=Microbial+Genomics"},"results":[{"id":"W2489242664","doi":"10.1099/mgen.0.000080","title":"Metagenomic data-mining reveals contrasting microbial populations responsible for trimethylamine formation in human gut and marine ecosystems","year":2016,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":73,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Waterloo","funders":"Natural Environment Research Council; Sight Research UK","keywords":"Metagenomics; Proteobacteria; Trimethylamine N-oxide; Betaine; Trimethylamine; Biology; Actinobacteria; Gut flora; Metabolic pathway; Euryarchaeota; Microbiology; Bacteria; Archaea; Biochemistry; Metabolism; 16S ribosomal RNA; Genetics; Gene","score_opus":0.05697683960279048,"score_gpt":0.31165418346154933,"score_spread":0.25467734385875884,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2489242664","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9735126,0.0076184007,0.0035813162,0.0004291305,0.000021985827,0.000028667597,0.0139331445,0.00012884181,0.0007459493],"genre_scores_gemma":[0.9731905,0.0030657419,0.006660406,0.00023106557,0.000018336117,0.00003422036,0.016424404,0.000041365594,0.00033397094],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.999474,0.000105678686,0.0000461794,0.0002160441,0.000073838404,0.0000842319],"domain_scores_gemma":[0.99960536,0.00010036955,0.00012576094,0.00004499991,0.000066687135,0.000056905836],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00059144106,0.0004480268,0.0006807665,0.0019864466,0.0003802438,0.0008587873,0.0002510307,0.00047228573,0.0007110026],"category_scores_gemma":[0.0010978344,0.0001963902,0.0009481045,0.0019171998,0.00019671199,0.00037748387,0.0009725338,0.0003782818,0.00026082675],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0015727729,0.00016213814,0.6843536,0.0023567542,0.0019283838,0.0011397492,0.0011773667,0.0017955421,0.21507458,0.00058356544,0.0025350365,0.08732051],"study_design_scores_gemma":[0.000032567576,0.00030011573,0.94634145,0.00029352584,0.0013311098,0.0019306015,0.0028334302,0.0059384564,0.025308372,0.001330554,0.014282291,0.000077478624],"about_ca_topic_score_codex":0.002616919,"about_ca_topic_score_gemma":0.0046047657,"teacher_disagreement_score":0.002616919,"about_ca_system_score_codex":0.0002798332,"about_ca_system_score_gemma":0.0005065703,"threshold_uncertainty_score":0.005203426},"labels":[],"label_agreement":null},{"id":"W2736246141","doi":"10.1099/mgen.0.000123","title":"Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Yersinia bacterium, plague, ectoparasites research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University","funders":"","keywords":"Yersinia pestis; Genome; Ancient DNA; Comparative genomics; Contig; Biology; Evolutionary biology; Synteny; Genomics; Rolling circle replication; Plague (disease); Genetics; Geography; Gene; Archaeology; Virulence","score_opus":0.03235628995941073,"score_gpt":0.30247863713326145,"score_spread":0.27012234717385075,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2736246141","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9258009,0.00037883292,0.07178795,0.00006446953,0.000017462413,0.000038215225,0.0005113664,0.000760024,0.00064080197],"genre_scores_gemma":[0.7107821,0.0002578996,0.28542203,0.000037080972,0.0000122370475,0.00009489677,0.0024512496,0.00041970526,0.00052281405],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9992194,0.00021762602,0.00006812446,0.00025141265,0.00015789806,0.000085455526],"domain_scores_gemma":[0.99892175,0.00049658323,0.00014411203,0.00018235928,0.00019577266,0.000059438735],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001445956,0.0006181912,0.00058329204,0.0011429176,0.00059878174,0.00078904,0.00046795968,0.0005846329,0.00072530704],"category_scores_gemma":[0.0038469234,0.00031892981,0.0008061708,0.0013459508,0.0004457002,0.00040603764,0.0008211171,0.0006886881,0.0002541874],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.001235463,0.0001308461,0.010538832,0.0005509647,0.00013350433,0.00053280534,0.0020568254,0.053020168,0.8210991,0.0016928902,0.0003520169,0.10865653],"study_design_scores_gemma":[0.00006848729,0.0007206491,0.07186791,0.00008439745,0.00021496098,0.0006416016,0.00091109966,0.43214235,0.48281732,0.0015573214,0.008857865,0.00011597713],"about_ca_topic_score_codex":0.0027555593,"about_ca_topic_score_gemma":0.0030928468,"teacher_disagreement_score":0.0027555593,"about_ca_system_score_codex":0.00044709523,"about_ca_system_score_gemma":0.00040369894,"threshold_uncertainty_score":0.007646978},"labels":[],"label_agreement":null},{"id":"W2743410431","doi":"10.1099/mgen.0.000127","title":"Broad-scale redistribution of mRNA abundance and transcriptional machinery in response to growth rate in Salmonella enterica serovar Typhimurium","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Regina","funders":"Natural Sciences and Engineering Research Council of Canada; Science Foundation Ireland","keywords":"Biology; Sigma factor; Transcription (linguistics); RNA polymerase; Salmonella enterica; rpoS; Exponential growth; Gene; Gene expression; Transcriptional regulation; Bacterial transcription; Cell biology; Genetics; RNA; Promoter; Escherichia coli","score_opus":0.0061772835491154515,"score_gpt":0.2186365147117336,"score_spread":0.21245923116261814,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2743410431","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9991097,0.00019494326,0.00040694157,0.000016814693,0.0000023370671,0.0000014457942,0.0001107242,0.000017008257,0.00014011086],"genre_scores_gemma":[0.99868375,0.0001352308,0.00056052575,0.000023263276,0.000002506745,0.000005278875,0.0002496139,0.0000162933,0.00032352627],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9999186,0.00001038046,0.0000061253763,0.000024084937,0.000019812653,0.00002107773],"domain_scores_gemma":[0.99979395,0.000050982522,0.000047575806,0.000026002723,0.000039075865,0.000042447125],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000108973996,0.0001487857,0.00018060088,0.00024798527,0.00006272515,0.00026657342,0.00009563389,0.00016793369,0.00023484544],"category_scores_gemma":[0.00019620378,0.00018446823,0.00017404559,0.00012072975,0.00019293482,0.00011700276,0.00017969427,0.00023855195,0.00014261967],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000094554794,0.0000054530815,0.0010123572,0.0000073138126,0.0000025023614,0.000010302224,0.000013747746,0.00007436939,0.99824846,0.000009228744,0.0000053309786,0.0005164245],"study_design_scores_gemma":[0.000021106107,0.00068134465,0.21526532,0.000010779195,0.000039697483,0.00019787997,0.0002137239,0.0049657077,0.7777018,0.000108356595,0.0007663469,0.000027922462],"about_ca_topic_score_codex":0.00102801,"about_ca_topic_score_gemma":0.0012320359,"teacher_disagreement_score":0.00102801,"about_ca_system_score_codex":0.00021606765,"about_ca_system_score_gemma":0.000093432645,"threshold_uncertainty_score":0.002044022},"labels":[],"label_agreement":null},{"id":"W2768173870","doi":"10.1099/mgen.0.000140","title":"Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Cystic Fibrosis Research Advances","field":"Medicine","cited_by":43,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Manitoba","funders":"","keywords":"Biology; Microbiology; Burkholderia; Burkholderia cenocepacia; Genome; Burkholderia cepacia complex; Envelope (radar); Bacteria; Genetics; Gene","score_opus":0.060021777304911476,"score_gpt":0.31070089067731466,"score_spread":0.2506791133724032,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2768173870","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99705255,0.00024555324,0.0013053168,0.000013469387,0.0000035464052,0.000007784666,0.0010998722,0.000024212757,0.00024775424],"genre_scores_gemma":[0.9948547,0.00015077801,0.0021749013,0.000016781094,0.0000014401436,0.000010557594,0.0024999562,0.000016835738,0.00027406483],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.99991786,0.000007678338,0.000010517347,0.000028064185,0.000019351595,0.000016560854],"domain_scores_gemma":[0.99984646,0.000036630994,0.00004695996,0.00001929909,0.000018661667,0.000031954383],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000074132986,0.00027646188,0.0002448892,0.0003952887,0.00014413075,0.0002064398,0.00013564645,0.00018085453,0.00048256878],"category_scores_gemma":[0.00024672,0.00010168693,0.00031815877,0.00037846089,0.00010260818,0.00013953292,0.00022997701,0.00021799999,0.00019363774],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00022141564,0.000020793597,0.004356535,0.000050818566,0.000011231863,0.00010116277,0.00003098707,0.00019473411,0.99312615,0.00004441958,0.000019000345,0.0018228384],"study_design_scores_gemma":[0.000044344735,0.00051114743,0.4134026,0.0000315617,0.00016298129,0.0020309202,0.0003807779,0.0085059395,0.5705948,0.00026983654,0.004029209,0.000035946],"about_ca_topic_score_codex":0.0011976446,"about_ca_topic_score_gemma":0.0011142239,"teacher_disagreement_score":0.0011976446,"about_ca_system_score_codex":0.00015545999,"about_ca_system_score_gemma":0.00013066709,"threshold_uncertainty_score":0.0023813248},"labels":[],"label_agreement":null},{"id":"W2782879881","doi":"10.1099/mgen.0.000151","title":"Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR)","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":63,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada","keywords":"In silico; Multilocus sequence typing; Salmonella; Genome; Whole genome sequencing; Biology; Typing; Serotype; Computational biology; Concordance; Genetics; Database; 1000 Genomes Project; Data quality; Data mining; Computer science; Gene; Microbiology; Genotype; Engineering","score_opus":0.2991486640787514,"score_gpt":0.3640092327917008,"score_spread":0.06486056871294937,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2782879881","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9568256,0.0017132226,0.019147702,0.0002035456,0.000047052265,0.00020278415,0.019316226,0.00064169976,0.0019020779],"genre_scores_gemma":[0.85988766,0.0013253237,0.05818654,0.00018498988,0.000032699958,0.00016825009,0.07914821,0.00032157445,0.0007447862],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99281824,0.0019413988,0.0012721057,0.001156753,0.0024339892,0.00037758902],"domain_scores_gemma":[0.97028035,0.009504649,0.0064284876,0.0046058074,0.008462458,0.00071816146],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.012040369,0.00063559634,0.00091857556,0.005188711,0.00095130573,0.002172216,0.0006389703,0.00063927,0.0012072496],"category_scores_gemma":[0.02558431,0.00051208044,0.0009974835,0.004476471,0.00063932734,0.0013918662,0.0019400165,0.00081753853,0.0008257283],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0015071973,0.0005596964,0.5373476,0.0026083668,0.0013413168,0.00064163,0.0028743905,0.00679006,0.32497728,0.0010466818,0.0041517457,0.11615394],"study_design_scores_gemma":[0.000063191044,0.0011415933,0.8283691,0.0007665702,0.00090046076,0.0012086388,0.0017462363,0.020219408,0.115673386,0.0009990279,0.028686237,0.0002261187],"about_ca_topic_score_codex":0.0031968046,"about_ca_topic_score_gemma":0.0070139645,"teacher_disagreement_score":0.012040369,"about_ca_system_score_codex":0.0005491826,"about_ca_system_score_gemma":0.0017403068,"threshold_uncertainty_score":0.0636763},"labels":[],"label_agreement":null},{"id":"W2783442164","doi":"10.1099/mgen.0.000148","title":"Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université Laval","funders":"","keywords":"Biology; Plasmid; Escherichia coli; Genetics; Gene; Antibiotic resistance; Genomic library; Microbiology; Antibiotics","score_opus":0.023362552367614555,"score_gpt":0.24196663095687615,"score_spread":0.2186040785892616,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2783442164","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.62806433,0.0020217176,0.3580511,0.00058255397,0.00015169129,0.0006366993,0.00477002,0.002413895,0.003307938],"genre_scores_gemma":[0.61230683,0.0025799922,0.37489536,0.000798859,0.00003809884,0.00064523576,0.0045154695,0.0006032969,0.0036168636],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.999114,0.00023886989,0.000078498255,0.00014526086,0.00033857554,0.000084825464],"domain_scores_gemma":[0.9991007,0.0004193713,0.00013821841,0.00012867633,0.00011766623,0.000095389216],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0012894223,0.00068267656,0.0008292296,0.00074749923,0.00028858637,0.00079555396,0.0006901987,0.00059939845,0.000661794],"category_scores_gemma":[0.0010810848,0.0005408476,0.0005853876,0.00050849665,0.0004288312,0.00029334484,0.0007081466,0.00091702864,0.000549036],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000038467584,0.000019009847,0.0002268827,0.00005116434,0.000014127027,0.00003507792,0.000013895771,0.00029191998,0.9966769,0.00011865179,0.000046852187,0.002466962],"study_design_scores_gemma":[0.00003607638,0.00036608436,0.0051429705,0.000017602171,0.00008446255,0.00054051954,0.000069850365,0.011611004,0.97505695,0.00047473205,0.0065670405,0.000032716733],"about_ca_topic_score_codex":0.0008909497,"about_ca_topic_score_gemma":0.0033361157,"teacher_disagreement_score":0.0012894223,"about_ca_system_score_codex":0.00047091529,"about_ca_system_score_gemma":0.00042935842,"threshold_uncertainty_score":0.006819248},"labels":[],"label_agreement":null},{"id":"W2794546640","doi":"10.1099/mgen.0.000212","title":"Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":46,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Fonds pour la Formation à la Recherche dans l’Industrie et dans l’Agriculture; Belgian Federal Science Policy Office; Fonds De La Recherche Scientifique - FNRS; University of Warwick; Université Laval","keywords":"Cyanobacteria; Metagenomics; Biology; Bacteroidetes; Axenic; Proteobacteria; Bacteria; Phylum; Microbiome; Genome; Phylogenomics; Evolutionary biology; Computational biology; 16S ribosomal RNA; Phylogenetics; Gene; Genetics; Clade","score_opus":0.009013207640059103,"score_gpt":0.2109385219542524,"score_spread":0.20192531431419328,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2794546640","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.95075095,0.0008452282,0.02030036,0.00016585374,0.000051486997,0.0002487941,0.025691299,0.00044916946,0.0014968532],"genre_scores_gemma":[0.761535,0.0015020958,0.131803,0.00028815222,0.000042581,0.00057838927,0.101448834,0.0006641348,0.0021378286],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9996489,0.000037887603,0.000033271022,0.0001256252,0.00009529041,0.00005900313],"domain_scores_gemma":[0.9997012,0.00006582864,0.000036916554,0.000047079895,0.00008469324,0.00006415647],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005284459,0.0007100354,0.00073944434,0.0011183305,0.00057254604,0.00075654424,0.00033811847,0.0003903993,0.00088820345],"category_scores_gemma":[0.00084863324,0.00040353194,0.0011514254,0.0011960058,0.00019054954,0.000505525,0.0009867991,0.00085345015,0.0007160747],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0002847144,0.000067159446,0.005970455,0.00022966307,0.000051908777,0.00013290078,0.00022913779,0.0005672594,0.9838071,0.000079004225,0.00019485639,0.008385838],"study_design_scores_gemma":[0.0001192824,0.0011113343,0.25346985,0.00016308526,0.0006540872,0.0010792142,0.0013372194,0.024516638,0.69567066,0.0008902617,0.02084919,0.00013923492],"about_ca_topic_score_codex":0.0017883742,"about_ca_topic_score_gemma":0.00314016,"teacher_disagreement_score":0.0017883742,"about_ca_system_score_codex":0.0002574545,"about_ca_system_score_gemma":0.00069705455,"threshold_uncertainty_score":0.0035559535},"labels":[],"label_agreement":null},{"id":"W2796622087","doi":"10.1099/mgen.0.000175","title":"Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Pneumonia and Respiratory Infections","field":"Medicine","cited_by":16,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Provincial Laboratory of Public Health; University of British Columbia; BC Centre for Disease Control; University of Alberta Hospital; Alberta Hospital Edmonton; University of Alberta","funders":"","keywords":"Biology; Streptococcus pneumoniae; Genome; Clade; Comparative genomics; Phylogenetic tree; Genetics; Genomics; Microbiology; Gene; Bacteria","score_opus":0.05584724043814365,"score_gpt":0.28933677495691207,"score_spread":0.23348953451876842,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2796622087","genre_codex":"empirical","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.58232814,0.001571208,0.40436944,0.0010050347,0.00016289669,0.000963173,0.0025076426,0.0014327748,0.0056596296],"genre_scores_gemma":[0.5945073,0.0006368427,0.39850807,0.000777532,0.000055707864,0.0006862118,0.0024122647,0.00012649504,0.0022895562],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.99853873,0.0005156462,0.000071405964,0.0003666782,0.00036963902,0.00013795518],"domain_scores_gemma":[0.999035,0.0004129853,0.00025885474,0.000074597534,0.0001488021,0.00006973389],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0011533811,0.00096176943,0.00080861314,0.00086667563,0.0002544141,0.0007317749,0.00046623746,0.0009882974,0.0007177161],"category_scores_gemma":[0.0021530339,0.0004790031,0.0005317942,0.000519699,0.0005731455,0.00047861517,0.00046285545,0.00086183427,0.00089318305],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00006383071,0.00011310699,0.0021661655,0.00008933244,0.000011822166,0.000030177616,0.00003787537,0.00072807405,0.986902,0.00050022174,0.00013491175,0.009222495],"study_design_scores_gemma":[0.00003252696,0.0009939387,0.011540347,0.000038746588,0.00005936361,0.0003863013,0.000096205054,0.015898408,0.96475375,0.0009480132,0.0052189836,0.00003344701],"about_ca_topic_score_codex":0.00042620033,"about_ca_topic_score_gemma":0.00088182965,"teacher_disagreement_score":0.0011533811,"about_ca_system_score_codex":0.00057730655,"about_ca_system_score_gemma":0.0006261452,"threshold_uncertainty_score":0.006099701},"labels":[],"label_agreement":null},{"id":"W2805821531","doi":"10.1099/mgen.0.000182","title":"The mechanisms that regulate Vibrio parahaemolyticus virulence gene expression differ between pathotypes","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McGill University; Health Canada","funders":"Health Canada; McGill University","keywords":"Vibrio parahaemolyticus; Virulence; Biology; Hemolysin; Microbiology; Gene; Virulence factor; Genetics; Bacteria","score_opus":0.015951317389070428,"score_gpt":0.24671822540286864,"score_spread":0.2307669080137982,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2805821531","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9956493,0.0011892235,0.001475189,0.00007705073,0.000012610867,0.000036666326,0.0009475973,0.00003672757,0.0005756528],"genre_scores_gemma":[0.99170095,0.0013652958,0.0038052902,0.000116989395,0.000016657597,0.000101907506,0.0018603968,0.000028053366,0.001004427],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.99967,0.00003785767,0.0000326592,0.000083030594,0.000058464353,0.00011792454],"domain_scores_gemma":[0.9996747,0.000102429796,0.00009858227,0.000024707955,0.0000654151,0.00003422455],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00016840704,0.00033872892,0.00042671402,0.00057902007,0.00013687232,0.00036349252,0.00014416264,0.00037830198,0.0004880634],"category_scores_gemma":[0.0003455438,0.0001807623,0.0004244233,0.0004903666,0.00027489645,0.00027693095,0.00027957212,0.0003451237,0.00023798355],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00009557512,0.000021535176,0.0065419218,0.000048619764,0.000008172038,0.00006879679,0.00006607068,0.00006780154,0.9916249,0.00003400768,0.000017550552,0.0014051413],"study_design_scores_gemma":[0.000024106326,0.00072038546,0.5682327,0.000031472377,0.000069547255,0.0009350091,0.0008782224,0.0012085616,0.42567754,0.0003922499,0.0018004314,0.000029743644],"about_ca_topic_score_codex":0.00058054057,"about_ca_topic_score_gemma":0.0006455696,"teacher_disagreement_score":0.00058054057,"about_ca_system_score_codex":0.00017079573,"about_ca_system_score_gemma":0.00021887475,"threshold_uncertainty_score":0.00163275},"labels":[],"label_agreement":null},{"id":"W2883838322","doi":"10.1099/mgen.0.000206","title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":978,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Public Health Agency of Canada","funders":"Government of Canada; Public Health Agency; Public Health Agency of Canada","keywords":"Plasmid; Suite; Replicon; Biology; Typing; Python (programming language); Genetics; Computational biology; Contig; Computer science; Genome; DNA; Gene; Operating system","score_opus":0.016630362046628704,"score_gpt":0.23396908025826985,"score_spread":0.21733871821164114,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2883838322","genre_codex":"software","genre_gemma":"software","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"software","genre_consensus":"software","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.012203723,0.0012176929,0.26850885,0.0003597249,0.00037015212,0.0006244247,0.10125013,0.61129624,0.004169093],"genre_scores_gemma":[0.031152569,0.0013968201,0.47576296,0.0007008962,0.00012639513,0.0027263504,0.3244317,0.15765801,0.0060442756],"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","domain_scores_codex":[0.99772733,0.00052633445,0.00034109267,0.00058458245,0.000607848,0.00021279426],"domain_scores_gemma":[0.99746656,0.0011388095,0.0004051205,0.0004008607,0.00040540882,0.00018331419],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004405399,0.0049734297,0.0028863994,0.0046079513,0.0015450786,0.0034947195,0.0043954677,0.0015438881,0.030457594],"category_scores_gemma":[0.009622858,0.0034567367,0.003745659,0.0021053634,0.00085464,0.0028703313,0.00444888,0.004322623,0.033512264],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0022711246,0.00045882002,0.011976337,0.0101670595,0.0021129574,0.0014694328,0.0025432708,0.020468894,0.05649718,0.011444736,0.6950427,0.18554749],"study_design_scores_gemma":[0.001179764,0.00051297934,0.015754772,0.0017648211,0.0006181289,0.002049714,0.00077616255,0.1900725,0.0800924,0.03315946,0.67312264,0.00089655136],"about_ca_topic_score_codex":0.003849548,"about_ca_topic_score_gemma":0.0044901343,"teacher_disagreement_score":0.030457594,"about_ca_system_score_codex":0.0010764289,"about_ca_system_score_gemma":0.0028301198,"threshold_uncertainty_score":0.1018908},"labels":[],"label_agreement":null},{"id":"W2895933668","doi":"10.1099/mgen.0.000227","title":"Genomic epidemiology of clinical Campylobacter spp. at a single health trust site","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":25,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Biotechnology and Biological Sciences Research Council; Medical Research Council; Public Health England; Trent University; Nottingham Trent University","keywords":"Campylobacteriosis; Campylobacter; Typing; Biology; Locus (genetics); Multilocus sequence typing; Genetics; Epidemiology; Single-nucleotide polymorphism; Lineage (genetic); Population; Whole genome sequencing; SNP; Genome; Medicine; Environmental health; Genotype; Gene; Pathology; Bacteria","score_opus":0.10120306638826508,"score_gpt":0.32426454638862295,"score_spread":0.22306148000035786,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2895933668","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99898916,0.000065598324,0.00008879771,0.000061305975,0.0000019962092,0.000021147556,0.00051448314,0.000005567844,0.00025187543],"genre_scores_gemma":[0.9992969,0.00006658293,0.00016349087,0.000027423483,0.000002081637,0.0000128809215,0.00023316072,0.0000021190629,0.00019533157],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99864537,0.00031628375,0.00012076199,0.0003965589,0.0002551088,0.0002659483],"domain_scores_gemma":[0.9956157,0.00068644685,0.0016409924,0.00028058866,0.00089189224,0.00088435796],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005277404,0.00024996884,0.00033066617,0.0011699559,0.00086528563,0.00077568257,0.00062870793,0.00042829706,0.0024340462],"category_scores_gemma":[0.0030589723,0.0003936433,0.0002148699,0.0017834319,0.00091517024,0.00036289333,0.0011694361,0.00037326684,0.00035929075],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000061539125,0.000024839455,0.99177504,0.000058384558,0.000033131644,0.0005355078,0.0022932915,0.00017065098,0.0021199863,0.00005564117,0.0002528524,0.0026191324],"study_design_scores_gemma":[0.0000032250132,0.00013602042,0.9955047,0.000021969254,0.00001086514,0.0003811603,0.0032744114,0.00024172921,0.00015450882,0.00001743299,0.00024691568,0.000006958366],"about_ca_topic_score_codex":0.28371692,"about_ca_topic_score_gemma":0.42694637,"teacher_disagreement_score":0.28371692,"about_ca_system_score_codex":0.0028147134,"about_ca_system_score_gemma":0.0028633482,"threshold_uncertainty_score":0.564131},"labels":[],"label_agreement":null},{"id":"W2897710284","doi":"10.1099/mgen.0.000217","title":"Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":31,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"BC Centre for Disease Control; University of British Columbia","funders":"National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research","keywords":"Mycobacterium tuberculosis; Concordance; Transmission (telecommunications); Biology; Genetic diversity; Outbreak; Phylogenetic tree; Genetics; Tuberculosis; False positive paradox; Single-nucleotide polymorphism; Evolutionary biology; Whole genome sequencing; Genome; Computational biology; Genotype; Virology; Medicine; Computer science; Population; Gene; Artificial intelligence; Environmental health","score_opus":0.04422785186587053,"score_gpt":0.3003772448659613,"score_spread":0.25614939300009076,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2897710284","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.98796207,0.0021459663,0.006380368,0.00013054111,0.000007686066,0.000018511068,0.0005829642,0.00003642184,0.0027355459],"genre_scores_gemma":[0.99640405,0.00034340104,0.0029295506,0.000034396555,0.000005029758,0.0000039479364,0.00016983072,0.000004619904,0.00010523168],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99894065,0.000493026,0.000051148578,0.00021566046,0.00017478745,0.00012466908],"domain_scores_gemma":[0.9981578,0.0010061838,0.00039412294,0.00015929261,0.00016177256,0.00012078007],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0019113373,0.00030757207,0.00040558807,0.0018678051,0.00090069044,0.001543304,0.00028065266,0.00039870973,0.0005421532],"category_scores_gemma":[0.0049873358,0.000236341,0.00023862973,0.0016483709,0.0007240536,0.00049686764,0.00053768134,0.00052903173,0.0001539791],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00013573254,0.000022372677,0.9399688,0.00012515769,0.00016968396,0.0002501489,0.0014751118,0.002514502,0.022828577,0.0007414588,0.00017363719,0.031594813],"study_design_scores_gemma":[0.000004723405,0.00005153034,0.9833244,0.00008402624,0.000079467696,0.0004938228,0.0011792628,0.006695033,0.0039651804,0.0022126515,0.0018908484,0.000018916355],"about_ca_topic_score_codex":0.052019965,"about_ca_topic_score_gemma":0.09729477,"teacher_disagreement_score":0.052019965,"about_ca_system_score_codex":0.00097225077,"about_ca_system_score_gemma":0.00079336995,"threshold_uncertainty_score":0.103434324},"labels":[],"label_agreement":null},{"id":"W2908694387","doi":"10.1099/mgen.0.000237","title":"Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria","year":2019,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Listeria monocytogenes in Food Safety","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Ste. Anne's Hospital; University of Guelph; BC Centre for Disease Control; Public Health Ontario; Health Canada; Public Health Agency of Canada","funders":"Public Health Agency; Public Health Agency of Canada; Canadian Food Inspection Agency","keywords":"Subtyping; Genome; Biology; Phylogenetic tree; Outbreak; Prophage; Genetics; Whole genome sequencing; Phylogenetics; Evolutionary biology; Virology; Gene; Bacteriophage","score_opus":0.10044842794727359,"score_gpt":0.38005359960921214,"score_spread":0.27960517166193855,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2908694387","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9039,0.0028765476,0.051698398,0.0013744663,0.00007878588,0.0002755105,0.03215154,0.000685561,0.006959142],"genre_scores_gemma":[0.92495966,0.0004662039,0.04645746,0.00028756552,0.000029941102,0.0001336033,0.026986124,0.00021181258,0.00046747102],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9922069,0.0030254535,0.0007736077,0.0018027747,0.0015896579,0.0006016532],"domain_scores_gemma":[0.9805644,0.00901886,0.002649232,0.003943008,0.0032491588,0.0005753617],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.009431633,0.000778485,0.0008104348,0.004125018,0.0012706352,0.00344699,0.0012872976,0.0008771335,0.0014304925],"category_scores_gemma":[0.027919658,0.0004160933,0.0010484493,0.0055994513,0.0010503983,0.0010651174,0.0032168678,0.001019396,0.0003378562],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0013726093,0.00021144043,0.7780783,0.0023610955,0.0030466667,0.0016352421,0.005087909,0.014966257,0.071880184,0.0074729095,0.0039039159,0.10998334],"study_design_scores_gemma":[0.00005090422,0.00015424078,0.949328,0.00037887925,0.00059542945,0.0008763021,0.0027211357,0.01302564,0.007661012,0.0071820007,0.017951606,0.00007478868],"about_ca_topic_score_codex":0.0367457,"about_ca_topic_score_gemma":0.09903729,"teacher_disagreement_score":0.0367457,"about_ca_system_score_codex":0.0024911205,"about_ca_system_score_gemma":0.0036034693,"threshold_uncertainty_score":0.07306361},"labels":[],"label_agreement":null},{"id":"W2949845804","doi":"10.1099/mgen.0.000219","title":"Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":21,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"","funders":"Engineering and Physical Sciences Research Council","keywords":"Immigration; Transmission (telecommunications); Tuberculosis; Quarter (Canadian coin); Demography; Incidence (geometry); Geography; Cluster (spacecraft); Population; Mycobacterium tuberculosis; Environmental health; Medicine; Pathology; Sociology","score_opus":0.03740897845494287,"score_gpt":0.30143777133320354,"score_spread":0.26402879287826064,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2949845804","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.8956226,0.0007665309,0.09801876,0.0008989542,0.000111207926,0.00008190712,0.0014548337,0.0001362483,0.002908849],"genre_scores_gemma":[0.9798232,0.00037588514,0.017470459,0.000118717435,0.000030195915,0.000057639834,0.0007164188,0.00003673975,0.0013708228],"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9993862,0.0003822677,0.000025567071,0.00011587112,0.00002127497,0.00006870506],"domain_scores_gemma":[0.99829715,0.0012832453,0.00019722483,0.000081026395,0.00006699743,0.000074359676],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0015376264,0.00059760985,0.0006335615,0.0006655808,0.00049774104,0.0010189998,0.00096724945,0.0011538343,0.0016411039],"category_scores_gemma":[0.0053270715,0.0003791127,0.0010687929,0.00062226463,0.00068213354,0.000854666,0.00068877445,0.0010128533,0.00022143095],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000372487,0.00015429934,0.13002515,0.00011363766,0.00033124845,0.000716096,0.001222058,0.8289004,0.002222305,0.020895688,0.0013739612,0.013672675],"study_design_scores_gemma":[0.00003390161,0.00007054647,0.0129978135,0.00002973894,0.000059512346,0.00015469945,0.00027874595,0.97423345,0.00015687807,0.010848899,0.001109955,0.000025794086],"about_ca_topic_score_codex":0.042568527,"about_ca_topic_score_gemma":0.029088408,"teacher_disagreement_score":0.042568527,"about_ca_system_score_codex":0.00094238424,"about_ca_system_score_gemma":0.0008357693,"threshold_uncertainty_score":0.084641516},"labels":[],"label_agreement":null},{"id":"W2951211878","doi":"10.1099/mgen.0.000116","title":"SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":162,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"BC Centre for Disease Control; Dalhousie University; Simon Fraser University; Health Canada; University of Manitoba; Public Health Agency of Canada","funders":"Genome British Columbia; Genome Canada","keywords":"Phylogenomics; Indel; Computational biology; Genome; Whole genome sequencing; Scalability; Biology; Workflow; Genomics; Pipeline (software); Computer science; Genetics; Data mining; Phylogenetic tree; Single-nucleotide polymorphism; Database; Clade; Gene; Operating system","score_opus":0.03370385685354935,"score_gpt":0.2675280396315327,"score_spread":0.23382418277798336,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2951211878","genre_codex":"software","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.0065357997,0.0015444085,0.4175891,0.0006845296,0.00031825402,0.00049080176,0.088107094,0.48046133,0.0042686732],"genre_scores_gemma":[0.036709543,0.0012197974,0.6702815,0.0011178365,0.00013906446,0.0017002879,0.20259085,0.08090473,0.0053363736],"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9978034,0.00050688285,0.00019821443,0.00067288225,0.00053026393,0.00028844512],"domain_scores_gemma":[0.9976058,0.0010953237,0.0002815372,0.0004582098,0.00034052282,0.00021871987],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004156222,0.003173167,0.0026578584,0.004544131,0.0014364778,0.0041426835,0.0042185755,0.0019663947,0.03316241],"category_scores_gemma":[0.0100109,0.0029050384,0.0045419727,0.0032312772,0.0009023126,0.0036672803,0.006061462,0.0050394265,0.026550287],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0026339418,0.00038824385,0.01514001,0.0064710854,0.0026921055,0.0014844132,0.0026590568,0.02099563,0.069282435,0.016650701,0.5647178,0.29688457],"study_design_scores_gemma":[0.0014798198,0.0003896782,0.017792447,0.0008717716,0.00067589595,0.0013283881,0.0004984763,0.23888901,0.058284275,0.062334508,0.6164794,0.0009762653],"about_ca_topic_score_codex":0.0073477803,"about_ca_topic_score_gemma":0.01038501,"teacher_disagreement_score":0.03316241,"about_ca_system_score_codex":0.0013481285,"about_ca_system_score_gemma":0.004171405,"threshold_uncertainty_score":0.110939324},"labels":[],"label_agreement":null},{"id":"W2951337360","doi":"10.1099/mgen.0.000142","title":"Vibrio cholerae genomic diversity within and between patients","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":41,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal","funders":"Canadian Institutes of Health Research; National Institutes of Health; National Institute of Diabetes and Digestive and Kidney Diseases; International Centre for Diarrhoeal Disease Research, Bangladesh; Canada Research Chairs; Styrelsen för Internationellt Utvecklingssamarbete; National Institute of Allergy and Infectious Diseases; Global Affairs Canada; Department for International Development; Robert Wood Johnson Foundation","keywords":"Vibrio cholerae; Cholera; Biology; Horizontal gene transfer; Cholera toxin; Genetics; Plasmid; Transmission (telecommunications); Gene; Population; El Tor; Genetic diversity; Point mutation; Genome; Microbiology; Mutation; Bacteria; Medicine","score_opus":0.01789418367661072,"score_gpt":0.24687776024981953,"score_spread":0.2289835765732088,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2951337360","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9992762,0.00010896888,0.00013502176,0.000029716604,0.0000019382817,0.0000073623723,0.00019033678,0.0000026270206,0.00024793224],"genre_scores_gemma":[0.99957556,0.00004753258,0.00009412906,0.000030307454,0.0000028634038,0.000007316324,0.0001726041,0.0000024324418,0.00006738164],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9991634,0.00018636374,0.00007685979,0.00033087694,0.000110742825,0.00013175365],"domain_scores_gemma":[0.9992519,0.00023770473,0.0002047625,0.000077574754,0.00009198351,0.00013612457],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002848795,0.00018327741,0.00036535203,0.00046933294,0.0004023993,0.00065532123,0.00017034245,0.00041722745,0.0011100391],"category_scores_gemma":[0.0026037944,0.00013850901,0.00015506249,0.0004898616,0.00048296756,0.00029466423,0.0006841994,0.0003418703,0.00014310559],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0004307658,0.000026460291,0.9775733,0.000024936731,0.000063396175,0.00069583434,0.0013585137,0.00014409918,0.012245299,0.00010264115,0.00018849468,0.007146422],"study_design_scores_gemma":[0.000013678877,0.00024752095,0.99276674,0.000013695299,0.000032268792,0.002715591,0.0012713169,0.00024603895,0.0014754399,0.00018522626,0.0010141816,0.00001835789],"about_ca_topic_score_codex":0.0017182161,"about_ca_topic_score_gemma":0.0013814488,"teacher_disagreement_score":0.0017182161,"about_ca_system_score_codex":0.00032085206,"about_ca_system_score_gemma":0.00016526671,"threshold_uncertainty_score":0.0037134886},"labels":[],"label_agreement":null},{"id":"W2951342755","doi":"10.1099/mgen.0.000088","title":"Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion","year":2016,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":32,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Public Health Agency of Canada","funders":"China Scholarship Council; Suomen Kulttuurirahasto; Academy of Finland; European Food Safety Authority","keywords":"Campylobacter jejuni; Biology; Genome; Lineage (genetic); Genetics; Multilocus sequence typing; Evolutionary biology; Microevolution; Population; Clade; Genotype; Whole genome sequencing; Phylogenetics; Gene","score_opus":0.02105712742544665,"score_gpt":0.2119918518245966,"score_spread":0.19093472439914994,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2951342755","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9994635,0.00007580752,0.00018913449,0.0000073843853,5.2541634e-7,0.000002631864,0.000045959638,0.000003892567,0.0002112674],"genre_scores_gemma":[0.9993782,0.000032891872,0.00034845978,0.000010536169,0.0000011334279,0.0000024776605,0.00010240937,0.0000023782343,0.00012144968],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9997693,0.000028645502,0.000017363078,0.00009410574,0.00003902392,0.000051609084],"domain_scores_gemma":[0.999539,0.00009826582,0.0001962538,0.00006958726,0.000044359047,0.000052597854],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00023522193,0.0001491307,0.00020278711,0.0007013077,0.00025100316,0.0003432383,0.00012806154,0.00029803402,0.0009309581],"category_scores_gemma":[0.0005222096,0.00014336291,0.00014066845,0.0007096985,0.00036100677,0.00019191086,0.00035697114,0.00020795864,0.000138094],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0004237387,0.00006453038,0.59930784,0.000069199705,0.00009568356,0.000301537,0.001324695,0.00039626803,0.3780241,0.00016959645,0.00013394527,0.019688925],"study_design_scores_gemma":[0.000002249075,0.000074667805,0.9958468,0.0000036149077,0.000013949044,0.00034113214,0.0002733231,0.00025473963,0.0028927028,0.00004998747,0.00024334261,0.0000035935589],"about_ca_topic_score_codex":0.0029377928,"about_ca_topic_score_gemma":0.0068419757,"teacher_disagreement_score":0.0029377928,"about_ca_system_score_codex":0.00018240434,"about_ca_system_score_gemma":0.00013668466,"threshold_uncertainty_score":0.0058413744},"labels":[],"label_agreement":null},{"id":"W2952882858","doi":"10.1099/mgen.0.000133","title":"Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis","year":2017,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Yersinia bacterium, plague, ectoparasites research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Trent University; European Defence Agency; Nottingham Trent University; Helsingin Yliopisto","keywords":"Yersinia pseudotuberculosis; Biology; Population; Phylogeography; Evolutionary biology; Yersinia; Lineage (genetic); Genetics; Biological dispersal; Population genomics; Comparative genomics; Genomics; Genome; Phylogenetics; Gene; Virulence; Bacteria","score_opus":0.009886683649280054,"score_gpt":0.2998115613193984,"score_spread":0.2899248776701183,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2952882858","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9993048,0.00006681378,0.00031868054,0.000010800767,5.832478e-7,0.0000023120538,0.00007148072,0.0000032822009,0.00022127978],"genre_scores_gemma":[0.9990447,0.00007717287,0.0004198548,0.000016978596,0.0000013156273,0.0000055592973,0.00034993805,0.000004087349,0.00008031385],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9998247,0.000042756885,0.000009531139,0.00007678784,0.00001655391,0.000029633951],"domain_scores_gemma":[0.9995813,0.00013632303,0.000121582714,0.00006375028,0.00005460849,0.000042528933],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00038415493,0.00013867857,0.00026478182,0.0010006675,0.00032820387,0.00044532475,0.00016784245,0.0002714293,0.0005872552],"category_scores_gemma":[0.00064209837,0.0001247228,0.00021971486,0.00085932994,0.00044459308,0.00025985003,0.00048105622,0.00034497472,0.00010801927],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0008218161,0.000097984346,0.78033423,0.00009286495,0.00032859214,0.0004330458,0.0040473184,0.0016442008,0.18377249,0.0008128492,0.00021433673,0.027400196],"study_design_scores_gemma":[0.000015301111,0.00011324875,0.9946267,0.000016541024,0.000056806843,0.00034959172,0.00092720083,0.0012385453,0.0016459308,0.00023666924,0.000759973,0.000013437667],"about_ca_topic_score_codex":0.0011263544,"about_ca_topic_score_gemma":0.0021896367,"teacher_disagreement_score":0.0011263544,"about_ca_system_score_codex":0.00018743766,"about_ca_system_score_gemma":0.00014608835,"threshold_uncertainty_score":0.002239585},"labels":[],"label_agreement":null},{"id":"W2953157660","doi":"10.1099/mgen.0.000146","title":"MentaLiST – A fast MLST caller for large MLST schemes","year":2018,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":63,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of British Columbia; BC Centre for Disease Control; Simon Fraser University","funders":"","keywords":"Multilocus sequence typing; Housekeeping gene; Genotyping; Typing; Computer science; Biology; Computational biology; Genetics; Gene; Genotype","score_opus":0.010939402114715165,"score_gpt":0.24507602436773868,"score_spread":0.2341366222530235,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2953157660","genre_codex":"methods","genre_gemma":"software","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"software","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.0071216817,0.0002430443,0.66573197,0.00019557899,0.00026193482,0.0002670279,0.004000195,0.31958705,0.0025914777],"genre_scores_gemma":[0.057579108,0.00026448397,0.8516802,0.00058533496,0.000113849404,0.0011616184,0.015203763,0.06552737,0.007884302],"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9970772,0.0005641862,0.00029457174,0.0007973342,0.00096994895,0.0002968778],"domain_scores_gemma":[0.9956943,0.0023709394,0.00030160032,0.0008060282,0.0006058067,0.00022135694],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0035251167,0.00257073,0.0019026407,0.001732929,0.0014596782,0.0028790885,0.0056401487,0.002926896,0.031117829],"category_scores_gemma":[0.01715227,0.0022523133,0.0027377205,0.0010248941,0.0009339533,0.002807686,0.0040455847,0.004342291,0.022556579],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0035498787,0.0005417925,0.009367596,0.002604574,0.0009821871,0.0013004218,0.0016375877,0.04952228,0.11366923,0.026994415,0.2710162,0.5188138],"study_design_scores_gemma":[0.0007576852,0.00024029601,0.0027202826,0.00023441213,0.00014960699,0.0008050218,0.00016950462,0.7020471,0.08879662,0.029315172,0.17419367,0.0005705912],"about_ca_topic_score_codex":0.0023068837,"about_ca_topic_score_gemma":0.0041821864,"teacher_disagreement_score":0.031117829,"about_ca_system_score_codex":0.0013688249,"about_ca_system_score_gemma":0.002274786,"threshold_uncertainty_score":0.10409951},"labels":[],"label_agreement":null},{"id":"W2962593936","doi":"10.1099/mgen.0.000282","title":"Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species","year":2019,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":29,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Fundação para a Ciência e a Tecnologia; Institute of Genetics; University of Tokyo; Ministry of Education, Culture, Sports, Science and Technology","keywords":"Recombination; Bacteriophage; Genome; Genetics; Biology; Gene; Escherichia coli","score_opus":0.005056656968780828,"score_gpt":0.1845271973813914,"score_spread":0.17947054041261057,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2962593936","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9885046,0.00031612357,0.010330565,0.000011604049,0.0000026739783,0.000009552161,0.0002961024,0.0000886038,0.00044014506],"genre_scores_gemma":[0.9855296,0.0001699004,0.012715729,0.000017558332,0.0000029210019,0.000018349298,0.0010657836,0.00004805322,0.00043213312],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99986076,0.00001852437,0.0000068319137,0.000056941222,0.000035551715,0.000021399459],"domain_scores_gemma":[0.99975866,0.000077084755,0.0000645644,0.000027715756,0.00004263049,0.000029325225],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00022932953,0.00020746827,0.00019257992,0.00056880544,0.00012726856,0.00028567205,0.00013832306,0.00023784267,0.0006430317],"category_scores_gemma":[0.0004601949,0.00010128879,0.0003009955,0.00043065991,0.00012582021,0.00020532127,0.00029873726,0.0002845391,0.00011837254],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00013418497,0.000020054102,0.010159107,0.00006751074,0.000030123381,0.00004582696,0.00007609229,0.00071142224,0.9793301,0.00020014467,0.00002965133,0.009195857],"study_design_scores_gemma":[0.000018289345,0.0007876238,0.43983826,0.000026517562,0.00015694072,0.0011029314,0.00025903172,0.034839883,0.5177267,0.0008561481,0.0043550557,0.000032604497],"about_ca_topic_score_codex":0.00045208415,"about_ca_topic_score_gemma":0.00039057,"teacher_disagreement_score":0.0006430317,"about_ca_system_score_codex":0.00011687242,"about_ca_system_score_gemma":0.00010570984,"threshold_uncertainty_score":0.0021511912},"labels":[],"label_agreement":null},{"id":"W2969856858","doi":"10.1099/mgen.0.000060","title":"Declaring a tuberculosis outbreak over with genomic epidemiology","year":2016,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":37,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of British Columbia; BC Centre for Disease Control; Interior Health","funders":"British Columbia Centre for Disease Control; Canada Research Chairs; Medical Research Council; Engineering and Physical Sciences Research Council; National Institute for Health and Care Research; Michael Smith Health Research BC","keywords":"Outbreak; Tuberculosis; Transmission (telecommunications); Infectious disease (medical specialty); Mycobacterium tuberculosis; Genome; Disease; Epidemiology; Public health; Virology; Biology; Pathogen; Molecular epidemiology; Medicine; Genetics; Genotype; Pathology; Gene; Computer science","score_opus":0.03251066751713301,"score_gpt":0.3012940226901891,"score_spread":0.2687833551730561,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2969856858","genre_codex":"methods","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.17061523,0.002178324,0.8119967,0.0045965924,0.00043370482,0.00020548128,0.0022948673,0.001870153,0.005808875],"genre_scores_gemma":[0.51392394,0.00071114104,0.48042575,0.00096612156,0.00038477225,0.000068161025,0.0023004073,0.00015495626,0.0010647993],"study_design_codex":"design_other","study_design_gemma":"observational","domain_scores_codex":[0.99651057,0.0014666548,0.00033372597,0.00096296764,0.000538834,0.00018723884],"domain_scores_gemma":[0.98713326,0.007447794,0.0026846891,0.0011477944,0.0011693237,0.00041720783],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0035333063,0.00061268156,0.00068528985,0.003193676,0.00078242185,0.0033563073,0.0010969578,0.0015762346,0.0011771247],"category_scores_gemma":[0.025171563,0.00044892178,0.00079670944,0.0022286898,0.00078572513,0.003139096,0.0019307617,0.0019267531,0.00036650393],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0007129576,0.00028355976,0.32006678,0.00070414087,0.00048897136,0.0026578738,0.0033430776,0.059857853,0.023460057,0.047408957,0.008287626,0.53272814],"study_design_scores_gemma":[0.00012604245,0.00040614003,0.11059157,0.000767224,0.00037581698,0.003888445,0.0034357975,0.5350755,0.01575497,0.24332729,0.08586936,0.0003818547],"about_ca_topic_score_codex":0.0036887184,"about_ca_topic_score_gemma":0.0051461128,"teacher_disagreement_score":0.0036887184,"about_ca_system_score_codex":0.0006252066,"about_ca_system_score_gemma":0.0012709765,"threshold_uncertainty_score":0.018686116},"labels":[],"label_agreement":null},{"id":"W2976577606","doi":"10.1099/mgen.0.000293","title":"Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients","year":2019,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":109,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McGill University","funders":"Biotechnology and Biological Sciences Research Council; Medical Research Council; Directorate for Biological Sciences; Surgical Reconstruction and Microbiology Research Centre; Quadram Institute Bioscience; National Institute for Health and Care Research","keywords":"Critically ill; Pathogen; Microbiology; Biology; Gut flora; Medicine; Intensive care medicine; Immunology","score_opus":0.004622400721439332,"score_gpt":0.20012658702649447,"score_spread":0.19550418630505514,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2976577606","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9995202,0.00018187732,0.00015381064,0.000021545913,0.0000018148694,0.000005667826,0.000043971184,0.0000019322242,0.00006923717],"genre_scores_gemma":[0.9995345,0.00010685727,0.00019877544,0.000034340388,0.0000058593973,0.0000055756773,0.00008013252,0.0000013305907,0.0000326868],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9993642,0.00017880303,0.00007360518,0.0001448132,0.00014452238,0.000094082854],"domain_scores_gemma":[0.99904937,0.0002153639,0.00038014152,0.000071837036,0.0001097961,0.00017342596],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00048011844,0.00026301906,0.0005182459,0.0006869563,0.00043050293,0.0007940102,0.00024173631,0.00039599568,0.00041224327],"category_scores_gemma":[0.0019378704,0.00020647701,0.0002950066,0.00057905016,0.00044041628,0.0004116526,0.0006652958,0.00048049187,0.00008322441],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00083905156,0.00013836959,0.9348879,0.0000741345,0.00009676461,0.0008708396,0.0006416926,0.00015104511,0.05235118,0.000038056067,0.0000712914,0.009839611],"study_design_scores_gemma":[0.0000060461684,0.0004143068,0.99386483,0.000009230128,0.000036423757,0.001389184,0.00044611812,0.00027692315,0.003343339,0.000037063775,0.00016840937,0.000008123852],"about_ca_topic_score_codex":0.0012771495,"about_ca_topic_score_gemma":0.0009689896,"teacher_disagreement_score":0.0012771495,"about_ca_system_score_codex":0.00020509429,"about_ca_system_score_gemma":0.00025150145,"threshold_uncertainty_score":0.002539456},"labels":[],"label_agreement":null},{"id":"W2982342360","doi":"10.1099/mgen.0.000300","title":"A survey of Fusobacterium nucleatum genes modulated by host cell infection","year":2019,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":27,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; University of British Columbia; Simon Fraser University; University of Guelph; BC Cancer Agency","funders":"BC Cancer Agency; Canadian Cancer Society Research Institute","keywords":"Fusobacterium nucleatum; Transcriptome; Biology; Gene; Microbiology; Host (biology); Inflammation; Cancer research; Gene expression; Immunology; Bacteria; Genetics; Porphyromonas gingivalis","score_opus":0.0062485442618143774,"score_gpt":0.20812540686557893,"score_spread":0.20187686260376456,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W2982342360","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.98469794,0.0027489366,0.004077125,0.00009964742,0.000031899417,0.00004606224,0.007128353,0.00007833284,0.0010917092],"genre_scores_gemma":[0.97844416,0.0028472226,0.00683614,0.00020345222,0.0000335982,0.00014268952,0.009244305,0.000034542423,0.0022139368],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9998412,0.00001643451,0.000010264308,0.000046771147,0.000042945903,0.000042445852],"domain_scores_gemma":[0.9998242,0.000045899513,0.00004529253,0.000011967759,0.000042883665,0.000029772851],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000112104026,0.0003020721,0.0003898169,0.0005768921,0.00030446146,0.0003301905,0.00008619951,0.00030676732,0.0006961162],"category_scores_gemma":[0.00022939012,0.00009930393,0.00027919977,0.000701283,0.00015476263,0.00020428922,0.00023252006,0.00026225633,0.00028433625],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000083701656,0.0000054013376,0.0017435377,0.000042151984,0.0000047610984,0.00004924538,0.000027216014,0.000029700534,0.99705136,0.000010343865,0.000027721007,0.0009249466],"study_design_scores_gemma":[0.000009434465,0.0006548839,0.3451454,0.000042554588,0.00009577879,0.0012920838,0.0007933702,0.001580497,0.6427434,0.0001777103,0.007428844,0.000036041016],"about_ca_topic_score_codex":0.0012213384,"about_ca_topic_score_gemma":0.001454488,"teacher_disagreement_score":0.0012213384,"about_ca_system_score_codex":0.00017760266,"about_ca_system_score_gemma":0.00017820571,"threshold_uncertainty_score":0.002428472},"labels":[],"label_agreement":null},{"id":"W3007426492","doi":"10.1099/mgen.0.000337","title":"Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":76,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal","funders":"Génome Québec; Genome Canada","keywords":"Genome-wide association study; Biology; Genetics; Locus (genetics); Population; Genetic association; Computational biology; Single-nucleotide polymorphism; Gene; Genotype","score_opus":0.021697274711796357,"score_gpt":0.2717327752966996,"score_spread":0.25003550058490326,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3007426492","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":"methods","model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":"methods","domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.7833327,0.0019331938,0.19967479,0.0014110015,0.00022917727,0.00025265917,0.0045895246,0.005952759,0.0026241858],"genre_scores_gemma":[0.7919759,0.00064068876,0.19640581,0.0005237449,0.000052617772,0.0004252793,0.008769529,0.00044841404,0.000758023],"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.996576,0.0024118435,0.00018599462,0.00044586972,0.00025359492,0.00012662327],"domain_scores_gemma":[0.96892625,0.026468487,0.000728457,0.0020260792,0.0013552775,0.0004954464],"candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.011837336,0.001170782,0.0011341182,0.0010914453,0.00069271,0.0012237272,0.0019518536,0.001788999,0.001868199],"category_scores_gemma":[0.027855152,0.0007243107,0.0015950669,0.001504276,0.0008139074,0.00080790924,0.0012807919,0.0017836129,0.0005175526],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00094292755,0.00023867731,0.022783324,0.00031387035,0.0006268998,0.00016000794,0.00019833253,0.9471438,0.0014009655,0.004052021,0.0020545807,0.020084629],"study_design_scores_gemma":[0.00020541945,0.00010034065,0.0021410536,0.000024381756,0.000039789884,0.000041605053,0.000045969402,0.9930975,0.0008806002,0.002594646,0.0008078449,0.000020832478],"about_ca_topic_score_codex":0.017627824,"about_ca_topic_score_gemma":0.013707782,"teacher_disagreement_score":0.98816264,"about_ca_system_score_codex":0.0009816871,"about_ca_system_score_gemma":0.0023539506,"threshold_uncertainty_score":0.06260258},"labels":[],"label_agreement":null},{"id":"W3009070426","doi":"10.1099/mgen.0.000341","title":"An assessment of genome annotation coverage across the bacterial tree of life","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":122,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Wilfrid Laurier University; University of Waterloo","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Annotation; Genome; Proteome; Biology; Bacterial genome size; Computational biology; Homology (biology); Genome project; Gene Annotation; Gene; Phylogenetics; Genome size; Genetics","score_opus":0.013214475990475446,"score_gpt":0.2681903846297509,"score_spread":0.2549759086392755,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3009070426","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9889181,0.0023651682,0.0054779816,0.00013524642,0.000008424412,0.00002046575,0.0018831049,0.00009907416,0.0010924377],"genre_scores_gemma":[0.9841188,0.0009692526,0.008193321,0.00007631444,0.000014419129,0.000045139328,0.0062314877,0.00005455258,0.00029666358],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99603516,0.0013118073,0.00044047448,0.00068030227,0.0011035184,0.0004287492],"domain_scores_gemma":[0.9789973,0.008415918,0.004947628,0.0016461334,0.005225079,0.0007679862],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00683344,0.00045594238,0.0006877774,0.005375257,0.00062491023,0.0017668835,0.0005348784,0.00050518464,0.000640173],"category_scores_gemma":[0.021066858,0.00027154243,0.0006355685,0.004188757,0.0005517156,0.0017857705,0.0015988147,0.00048591412,0.00034009732],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00090638245,0.000050570445,0.84573996,0.00074694696,0.0006446099,0.00018297479,0.0020339796,0.0035036558,0.09609839,0.0007073841,0.00041398808,0.048971254],"study_design_scores_gemma":[0.0000052169726,0.00026071072,0.98036283,0.000079526006,0.00016029619,0.00032584803,0.0008319579,0.005352823,0.008627698,0.00061995134,0.003340732,0.00003250409],"about_ca_topic_score_codex":0.0013493424,"about_ca_topic_score_gemma":0.0015875206,"teacher_disagreement_score":0.00683344,"about_ca_system_score_codex":0.0003852098,"about_ca_system_score_gemma":0.00056153897,"threshold_uncertainty_score":0.03613907},"labels":[],"label_agreement":null},{"id":"W3013494640","doi":"10.1099/mgen.0.000348","title":"Two cases of type-a Haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial Infections and Vaccines","field":"Immunology and Microbiology","cited_by":6,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal","funders":"Institute of Infection and Immunity; Canadian Institutes of Health Research; Canada Research Chairs","keywords":"Haemophilus influenzae; Meningitis; Haemophilus; Microbiology; Gene; Capsule; Medicine; Biology; Genetics; Pediatrics; Bacteria; Antibiotics","score_opus":0.02736911642500804,"score_gpt":0.23778734697943957,"score_spread":0.21041823055443154,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3013494640","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9961279,0.0003913798,0.0005016711,0.0005285157,0.00010398293,0.00007897103,0.00020052737,0.000027173104,0.0020398768],"genre_scores_gemma":[0.998257,0.0002644483,0.0004008636,0.00028416843,0.00010150887,0.000017233588,0.000252667,0.000008251223,0.00041389972],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99924916,0.000075751595,0.0000916638,0.0002764427,0.000086963424,0.00021992422],"domain_scores_gemma":[0.99873894,0.00016889734,0.00042310276,0.0001072619,0.00011076463,0.00045103164],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00022697171,0.0011906793,0.00052885205,0.0010610699,0.001418069,0.00095339457,0.0008873372,0.0023180654,0.0015177346],"category_scores_gemma":[0.0015780538,0.0007845004,0.00086783175,0.0006034827,0.0010228232,0.00092308957,0.0010985662,0.0017441126,0.0004036464],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00038218693,0.0003471282,0.59227175,0.00013364943,0.00013911384,0.38890445,0.0036698747,0.00020420329,0.0051481063,0.00028153596,0.0016100786,0.0069079474],"study_design_scores_gemma":[0.00006193554,0.0005651762,0.33879966,0.000108018634,0.000083805186,0.6499177,0.0036581408,0.00039163345,0.0025042295,0.00015222293,0.003689957,0.00006747062],"about_ca_topic_score_codex":0.00856441,"about_ca_topic_score_gemma":0.011734244,"teacher_disagreement_score":0.00856441,"about_ca_system_score_codex":0.0015491564,"about_ca_system_score_gemma":0.0005398006,"threshold_uncertainty_score":0.017029107},"labels":[],"label_agreement":null},{"id":"W3014721356","doi":"10.1099/mgen.0.000361","title":"Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":50,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"BC Centre for Disease Control; University of British Columbia","funders":"Biotechnology and Biological Sciences Research Council; Medical Research Council; Wellcome Trust","keywords":"Transmission (telecommunications); Mycobacterium tuberculosis; Genome; Biology; Tuberculosis; Computational biology; Transmissibility (structural dynamics); Genetics; Medicine; Computer science; Gene","score_opus":0.017779246365044896,"score_gpt":0.27017319017339375,"score_spread":0.25239394380834884,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3014721356","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99058175,0.0005350546,0.006690094,0.00039307057,0.0000058576306,0.000011364044,0.0014270177,0.000066190856,0.00028949685],"genre_scores_gemma":[0.9940118,0.00018982636,0.0032860874,0.000040284376,0.0000051736047,0.000010970952,0.0022053532,0.000016399792,0.00023406763],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9994332,0.00028289828,0.00003112957,0.00014145447,0.000031988187,0.00007936974],"domain_scores_gemma":[0.9978527,0.001037266,0.0004842418,0.00020338764,0.00028001456,0.00014242835],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0018174846,0.0003193071,0.00037228139,0.0013033703,0.0006484063,0.0010647137,0.0007486031,0.0006514694,0.0012817357],"category_scores_gemma":[0.008267761,0.00048094068,0.00065578416,0.0012927018,0.0005050328,0.000720667,0.0011187108,0.00083854137,0.0002415656],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00020619869,0.000043026328,0.8961987,0.00013266661,0.0005040879,0.00057509984,0.0015309072,0.075369745,0.0021799195,0.0021832066,0.0014620164,0.019614343],"study_design_scores_gemma":[0.000039207338,0.0000700856,0.5775602,0.00016179468,0.00024769144,0.0006072832,0.0017640847,0.41023076,0.00072799245,0.0037556235,0.004775821,0.000059461592],"about_ca_topic_score_codex":0.07822188,"about_ca_topic_score_gemma":0.080001034,"teacher_disagreement_score":0.07822188,"about_ca_system_score_codex":0.0012347326,"about_ca_system_score_gemma":0.00092581304,"threshold_uncertainty_score":0.1555332},"labels":[],"label_agreement":null},{"id":"W3031542094","doi":"10.1099/mgen.0.000376","title":"Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Canadian Food Inspection Agency; Public Health Agency of Canada","funders":"Government of Canada; Canadian Food Inspection Agency","keywords":"VTEC; Biology; Serotype; Herd; Outbreak; Genetics; Genome; Genotyping; Genotype; Escherichia coli; Microbiology; Virology; Gene; Animal science","score_opus":0.020264445737731368,"score_gpt":0.25263071834633594,"score_spread":0.23236627260860457,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3031542094","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9989083,0.00011599543,0.00011122305,0.000024939594,0.0000019047274,0.000008851805,0.0005450983,0.0000031009174,0.0002805258],"genre_scores_gemma":[0.9983827,0.00014672837,0.00024389713,0.000022679693,0.0000014918631,0.00000570494,0.0007331673,0.0000029599155,0.00046067784],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9989661,0.00006981093,0.000033766086,0.00032345884,0.0002662385,0.00034051808],"domain_scores_gemma":[0.9983255,0.00013917171,0.00027146406,0.000061501865,0.0007667449,0.00043553355],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00052149885,0.00022185362,0.00036196012,0.0016491265,0.0017014869,0.001322232,0.00086579256,0.00036461593,0.0010021137],"category_scores_gemma":[0.0016646668,0.00026799206,0.00032977774,0.0027660013,0.0007811837,0.00024844674,0.00056931446,0.0004412464,0.00010920826],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00016081911,0.000024503248,0.9900384,0.000016362455,0.000064073094,0.00012902364,0.0015540798,0.00022144367,0.0030477997,0.00005791796,0.00016946759,0.004515997],"study_design_scores_gemma":[0.0000013751282,0.00002864974,0.99846965,0.0000048336797,0.000010296098,0.000038550123,0.0008798476,0.00022218046,0.00009075298,0.0000063377697,0.00024375675,0.000003737587],"about_ca_topic_score_codex":0.95895123,"about_ca_topic_score_gemma":0.97422564,"teacher_disagreement_score":0.041048765,"about_ca_system_score_codex":0.013493877,"about_ca_system_score_gemma":0.006623291,"threshold_uncertainty_score":0.0979054},"labels":[],"label_agreement":null},{"id":"W3046304094","doi":"10.1099/mgen.0.000418","title":"Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":38,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University","funders":"National Institute of Allergy and Infectious Diseases; Engineering and Physical Sciences Research Council; National Institutes of Health","keywords":"Identification (biology); Biology; Mycobacterium tuberculosis; Transmission (telecommunications); Computational biology; Phylogenetic tree; Pairwise comparison; Genetics; Tuberculosis; Data mining; Computer science; Artificial intelligence; Gene; Medicine","score_opus":0.035843239650420536,"score_gpt":0.3215563427832443,"score_spread":0.2857131031328238,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3046304094","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":"methods","model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":"methods","domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.7894927,0.0012106441,0.20435907,0.00090594054,0.00016114021,0.00016442312,0.00040158178,0.0011197045,0.0021847924],"genre_scores_gemma":[0.9044913,0.00020663964,0.093401104,0.0006694295,0.000030426549,0.00009099253,0.0005231991,0.0002566696,0.00033030493],"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9765644,0.012941003,0.0014101693,0.005589617,0.0025570835,0.00093777484],"domain_scores_gemma":[0.9109002,0.07392624,0.0042437334,0.00691911,0.003433109,0.0005776289],"candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.038007885,0.001163797,0.0010074606,0.0013205104,0.0015067777,0.0029128555,0.0015797677,0.0023351037,0.0009114037],"category_scores_gemma":[0.12734327,0.00074973144,0.0019320789,0.0014164053,0.0017045229,0.0026698096,0.0017498196,0.0029682654,0.0004133579],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0019024808,0.00058474566,0.4124251,0.0008204683,0.0024615214,0.00073342834,0.0044640843,0.1957783,0.09520065,0.016119868,0.0026563776,0.26685306],"study_design_scores_gemma":[0.00018349243,0.000837404,0.14733945,0.00030195227,0.0013553796,0.0009186881,0.0013721688,0.70930254,0.09368053,0.03734998,0.0070157787,0.00034265278],"about_ca_topic_score_codex":0.0065393825,"about_ca_topic_score_gemma":0.007268608,"teacher_disagreement_score":0.96199214,"about_ca_system_score_codex":0.0013890265,"about_ca_system_score_gemma":0.0016571592,"threshold_uncertainty_score":0.2010073},"labels":[],"label_agreement":null},{"id":"W3088602524","doi":"10.1099/mgen.0.000435","title":"Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":162,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Public Health Agency of Canada","funders":"Public Health Agency of Canada","keywords":"Typing; Host (biology); Sequence (biology); Plasmid; Computational biology; Epidemiology; Computer science; Biology; Genetics; Medicine; Gene","score_opus":0.03315186555051549,"score_gpt":0.2400241374756805,"score_spread":0.206872271925165,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3088602524","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.69149625,0.0036605569,0.27031878,0.0003709972,0.00015772598,0.00028849623,0.024597729,0.0044690263,0.004640489],"genre_scores_gemma":[0.6866739,0.0012517119,0.281209,0.00018833647,0.000068533715,0.0002952018,0.02848094,0.00056896615,0.0012634628],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9977133,0.0006009554,0.00023607186,0.00073854014,0.00050380785,0.00020729184],"domain_scores_gemma":[0.9932974,0.0020871814,0.0018890976,0.00075717515,0.0014023836,0.0005667582],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0035359466,0.0009788447,0.0012020842,0.004233768,0.00045470087,0.0016082006,0.0009840179,0.0007850051,0.0020088265],"category_scores_gemma":[0.01155499,0.00044433822,0.0009663413,0.0039631003,0.00042987778,0.0013418371,0.0017900646,0.0009622089,0.0019239299],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.002501919,0.0004575658,0.41085765,0.00237016,0.00058726897,0.0006400397,0.0013287313,0.022142924,0.25589004,0.004274529,0.009179672,0.2897695],"study_design_scores_gemma":[0.00012282771,0.0012863403,0.41162267,0.00086362864,0.00067747437,0.0027416525,0.001421693,0.36290097,0.15071705,0.015652694,0.051577594,0.00041553818],"about_ca_topic_score_codex":0.0020964784,"about_ca_topic_score_gemma":0.0022828192,"teacher_disagreement_score":0.004233768,"about_ca_system_score_codex":0.00048574395,"about_ca_system_score_gemma":0.00092979905,"threshold_uncertainty_score":0.018700063},"labels":[],"label_agreement":null},{"id":"W3090089243","doi":"10.1099/mgen.0.000436","title":"Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":158,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University; Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Simon Fraser University; Genome Canada","keywords":"Metagenomics; Mobile genetic elements; Genome; Plasmid; Biology; Computational biology; Gene; Genetics; Genomic island; Bacterial genome size","score_opus":0.02411335039797261,"score_gpt":0.271351883816275,"score_spread":0.2472385334183024,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3090089243","genre_codex":"methods","genre_gemma":"empirical","domain_codex":null,"domain_gemma":"methods","model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":null,"domain_candidate":"methods","domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.25958726,0.0045898245,0.70569974,0.00057570887,0.00047209385,0.00029923322,0.004654656,0.020404488,0.0037169033],"genre_scores_gemma":[0.45957005,0.0013143832,0.51671064,0.0006705023,0.000047958667,0.00050865527,0.015484407,0.004080843,0.0016125492],"study_design_codex":"simulation_or_modeling","study_design_gemma":"observational","domain_scores_codex":[0.9983563,0.00051980757,0.00012708789,0.00043444455,0.0004452568,0.00011709928],"domain_scores_gemma":[0.9974366,0.0012818475,0.00022378417,0.0004607338,0.0005001948,0.0000968524],"candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.0032072207,0.001875998,0.0013725073,0.0008912826,0.0010970002,0.0016964944,0.0012393727,0.0010179548,0.0024861877],"category_scores_gemma":[0.008658877,0.00086469634,0.0030101573,0.0016313631,0.0006680656,0.0017885545,0.0010850324,0.0020007961,0.001912309],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.002402312,0.00043074155,0.06432232,0.0045466986,0.0032064703,0.0005670613,0.001166968,0.3282244,0.2539381,0.009689582,0.012673947,0.31883144],"study_design_scores_gemma":[0.00012881133,0.00054970745,0.030172806,0.0002829433,0.00061014853,0.00040933696,0.00045984166,0.7521745,0.1734382,0.015514943,0.026011258,0.00024747028],"about_ca_topic_score_codex":0.006701695,"about_ca_topic_score_gemma":0.011990098,"teacher_disagreement_score":0.9967928,"about_ca_system_score_codex":0.0009867526,"about_ca_system_score_gemma":0.0018743147,"threshold_uncertainty_score":0.016961634},"labels":[],"label_agreement":null},{"id":"W3092687430","doi":"10.1099/mgen.0.000454","title":"Azithromycin resistance mutations in Streptococcus pneumoniae as revealed by a chemogenomic screen","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Pneumonia and Respiratory Infections","field":"Medicine","cited_by":6,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université Laval","funders":"Canadian Institutes of Health Research","keywords":"23S ribosomal RNA; Streptococcus pneumoniae; Mutagenesis; Azithromycin; Biology; Glutamine; Mutant; Gene; Ribosomal RNA; Mutation; Genetics; Microbiology; Phenotype; Ribosomal protein; Bacterial genetics; Antibiotics; RNA; Escherichia coli; Ribosome; Amino acid","score_opus":0.013492953180228888,"score_gpt":0.24808786470800448,"score_spread":0.2345949115277756,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3092687430","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.97308695,0.0018451129,0.015199046,0.00023852078,0.000047516452,0.00017406324,0.0065644723,0.00055369595,0.0022905858],"genre_scores_gemma":[0.9658652,0.0014519561,0.02394054,0.0002675074,0.000016283218,0.00011349131,0.005802645,0.00014624558,0.002396195],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9996402,0.000038577946,0.000023608442,0.000097188466,0.00016087058,0.000039515853],"domain_scores_gemma":[0.999772,0.00005609276,0.000061517014,0.000028305343,0.00005246076,0.000029713181],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002082652,0.00046852723,0.000529202,0.0005026715,0.00020293491,0.00036124792,0.0002734126,0.0004408138,0.0006815721],"category_scores_gemma":[0.00048644433,0.00016320757,0.0003410194,0.0005081299,0.00016538621,0.00012604344,0.0003207493,0.00029441685,0.00034462626],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000037994127,0.000020096715,0.0013023344,0.000046390283,0.000016337797,0.00007231179,0.000016719561,0.00011509266,0.99489355,0.000023192542,0.00005102396,0.003404942],"study_design_scores_gemma":[0.000010762898,0.0006027664,0.06749594,0.00002386196,0.00016488762,0.0015403104,0.00013330231,0.005483482,0.91850066,0.00013889778,0.0058669136,0.00003818731],"about_ca_topic_score_codex":0.0010385845,"about_ca_topic_score_gemma":0.0024101038,"teacher_disagreement_score":0.0010385845,"about_ca_system_score_codex":0.00022509247,"about_ca_system_score_gemma":0.0002178396,"threshold_uncertainty_score":0.002280116},"labels":[],"label_agreement":null},{"id":"W3096284905","doi":"10.1099/mgen.0.000462","title":"Transcriptomics reveal core activities of the plant growth-promoting bacterium Delftia acidovorans RAY209 during interaction with canola and soybean roots","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Plant-Microbe Interactions and Immunity","field":"Agricultural and Biological Sciences","cited_by":23,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Saskatchewan Research Council (Canada); University of Saskatchewan; Lallemand (Canada); University of Regina","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Canola; Colonization; Biology; Transcriptome; Gene; Microbiology; Botany; Gene expression; Genetics","score_opus":0.020169827450184665,"score_gpt":0.18296935952637056,"score_spread":0.1627995320761859,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3096284905","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9894091,0.0014793583,0.0013208005,0.00010872896,0.000021094518,0.000030215868,0.0060479594,0.00007679071,0.0015059637],"genre_scores_gemma":[0.98018724,0.0012286804,0.003338836,0.00024219313,0.000020585729,0.00015257022,0.010026199,0.00006438445,0.0047393213],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.99986875,0.000006531643,0.000005013671,0.00005332764,0.00003266145,0.00003371827],"domain_scores_gemma":[0.9999155,0.000020236414,0.000021730033,0.0000048084858,0.000020276922,0.000017505174],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000104988445,0.00033416835,0.00046712227,0.00038980058,0.00023985258,0.00043306968,0.00011904889,0.0003666107,0.00069812295],"category_scores_gemma":[0.00014549501,0.00021006828,0.00035485663,0.00040090506,0.0001740715,0.00026775812,0.00031216728,0.00046491536,0.0003367558],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00010196529,0.000006918157,0.0012090838,0.000049823986,0.000005116291,0.00003517974,0.00005793165,0.000035542627,0.99758816,0.000026145328,0.000033980992,0.0008501773],"study_design_scores_gemma":[0.000027409327,0.000686296,0.57054526,0.00006920683,0.00012855239,0.00053955393,0.0014524218,0.0044931388,0.41412944,0.00033801538,0.007530521,0.000060113143],"about_ca_topic_score_codex":0.0018405023,"about_ca_topic_score_gemma":0.003140587,"teacher_disagreement_score":0.0018405023,"about_ca_system_score_codex":0.00024398237,"about_ca_system_score_gemma":0.00020574986,"threshold_uncertainty_score":0.0036596656},"labels":[],"label_agreement":null},{"id":"W3102341444","doi":"10.1099/mgen.0.000450","title":"Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data","year":2020,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":16,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University","funders":"Engineering and Physical Sciences Research Council; Government of Canada; Medical Research Council; Australian Government","keywords":"Outbreak; Transmission (telecommunications); Bayesian probability; Disease transmission; Tuberculosis; Computer science; Statistics; Geography; Data mining; Medicine; Data science; Artificial intelligence; Virology; Pathology; Mathematics; Telecommunications","score_opus":0.10610333598024754,"score_gpt":0.3581701923962637,"score_spread":0.2520668564160161,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3102341444","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9837479,0.00026037067,0.013224033,0.0011672644,0.000010613537,0.000035981848,0.0003959127,0.000055409055,0.0011024899],"genre_scores_gemma":[0.99218446,0.0002116488,0.00614953,0.00006461021,0.000014070018,0.000049707975,0.0004095878,0.000023623641,0.00089270703],"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.99897254,0.00070784497,0.000050660223,0.0001128442,0.000043627137,0.00011259911],"domain_scores_gemma":[0.97999567,0.017352514,0.001600307,0.00040288267,0.00035468806,0.00029395253],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0038014848,0.0006727531,0.0006972323,0.0013942982,0.0006256045,0.001126392,0.0014173384,0.0013388207,0.0017303622],"category_scores_gemma":[0.013916525,0.0005192625,0.001312207,0.0009836602,0.0011623263,0.0011928157,0.0011409922,0.0012613714,0.0002204905],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00027996206,0.00021185835,0.062130187,0.00013280612,0.00032356667,0.0014182429,0.000808126,0.91530424,0.0008975984,0.0125554325,0.0010796712,0.004858265],"study_design_scores_gemma":[0.000046800684,0.00007155899,0.0068845884,0.000014944281,0.000043215256,0.000115524796,0.00022545693,0.9901426,0.00013733911,0.0020830191,0.00020848315,0.000026351834],"about_ca_topic_score_codex":0.049926836,"about_ca_topic_score_gemma":0.023791892,"teacher_disagreement_score":0.049926836,"about_ca_system_score_codex":0.0025818495,"about_ca_system_score_gemma":0.0008250747,"threshold_uncertainty_score":0.09927249},"labels":[],"label_agreement":null},{"id":"W3119590930","doi":"10.1099/mgen.0.000500","title":"Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Dalhousie University; McMaster University","funders":"Canadian Institutes of Health Research; Cisco Systems Canada; Genome Canada; McMaster University; Cisco Systems","keywords":"Phenotype; In silico; Computational biology; Pseudomonas aeruginosa; Antibiotic resistance; Biology; Gene; Antimicrobial; Genome; Multiple drug resistance; Substrate (aquarium); Genetics; Drug resistance; Microbiology; Bacteria","score_opus":0.02100056784321435,"score_gpt":0.24885103213731033,"score_spread":0.22785046429409597,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3119590930","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.8075628,0.0009271294,0.18612549,0.00039456357,0.000031049865,0.00008761221,0.001236643,0.0016533087,0.0019813231],"genre_scores_gemma":[0.9495094,0.00048106397,0.04821202,0.00005816601,0.000009033934,0.000060008166,0.0012525056,0.00006148924,0.00035626994],"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9996476,0.00015733171,0.000025532794,0.000087650915,0.000054836946,0.00002708918],"domain_scores_gemma":[0.9987608,0.0009698233,0.00011848015,0.000042328676,0.00007828126,0.000030404288],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008404696,0.000994151,0.0009141288,0.00070897955,0.00017668078,0.0011764348,0.00051438535,0.00067413424,0.00055120024],"category_scores_gemma":[0.0024527013,0.00033654526,0.0009076076,0.00045871086,0.00023534666,0.00045109406,0.0002836626,0.00061313284,0.00032555],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0002053003,0.0002014122,0.025631377,0.00021367692,0.00013761158,0.00025796168,0.00005104177,0.9200401,0.029404512,0.00093909464,0.0003838647,0.022534082],"study_design_scores_gemma":[0.0000059645013,0.00005138332,0.0009051489,0.000006473615,0.000032075655,0.000034665583,0.000007833852,0.9943199,0.004032683,0.00038695429,0.00021006913,0.0000067451565],"about_ca_topic_score_codex":0.0019020803,"about_ca_topic_score_gemma":0.0023205425,"teacher_disagreement_score":0.0019020803,"about_ca_system_score_codex":0.0005604164,"about_ca_system_score_gemma":0.00059939356,"threshold_uncertainty_score":0.004444897},"labels":[],"label_agreement":null},{"id":"W3127018168","doi":"10.1099/mgen.0.000511","title":"Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Cystic Fibrosis Research Advances","field":"Medicine","cited_by":22,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Université Laval","funders":"National Health and Medical Research Council; Cystic Fibrosis Trust; Cystic Fibrosis Canada","keywords":"Prophage; Biology; Genome; Lineage (genetic); Phylogenetic tree; Population genomics; Genetics; Whole genome sequencing; Clade; Strain (injury); Comparative genomics; Population; Multilocus sequence typing; Genomics; Gene; Genotype; Medicine; Bacteriophage","score_opus":0.01812040175098389,"score_gpt":0.26241978494404955,"score_spread":0.24429938319306566,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3127018168","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99904925,0.00021083976,0.0001295325,0.000022567323,0.0000011853539,0.000006794103,0.00014367385,0.0000028852446,0.0004332484],"genre_scores_gemma":[0.9989115,0.00028021357,0.00020075565,0.000029872577,0.000002500177,0.0000074432937,0.00033442894,0.0000034753718,0.000229863],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9995907,0.00005825024,0.000026599206,0.00010805841,0.00008601032,0.00013041246],"domain_scores_gemma":[0.9996076,0.00006657398,0.00014211853,0.000034212535,0.00009736916,0.000052065494],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00023463483,0.00023001472,0.00018822248,0.0006498245,0.0004974384,0.0006643865,0.00023267065,0.0002791987,0.00074543065],"category_scores_gemma":[0.0009898267,0.00015573077,0.00015257807,0.00084662385,0.00031790798,0.00029446036,0.0006018603,0.00037088586,0.00018727689],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00095949013,0.00010940006,0.7613214,0.00018461377,0.000086006294,0.0029379292,0.005636242,0.00051639765,0.19803643,0.00044228655,0.00070376304,0.029066082],"study_design_scores_gemma":[0.0000062939607,0.0000896871,0.99510515,0.00001781906,0.000015090696,0.0008295219,0.0011417097,0.00028751016,0.0017520429,0.00004204139,0.00069909194,0.000014072329],"about_ca_topic_score_codex":0.0794367,"about_ca_topic_score_gemma":0.05964043,"teacher_disagreement_score":0.0794367,"about_ca_system_score_codex":0.00079389475,"about_ca_system_score_gemma":0.0007464169,"threshold_uncertainty_score":0.15794861},"labels":[],"label_agreement":null},{"id":"W3127818056","doi":"10.1099/mgen.0.000517","title":"Genera specific distribution of DEAD-box RNA helicases in cyanobacteria","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Helicase; RNA Helicase A; RNA; Degradosome; Genetics; Phylogenetic tree; Gene; Non-coding RNA","score_opus":0.011226696872299788,"score_gpt":0.2147514515579521,"score_spread":0.20352475468565231,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3127818056","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9935922,0.002404072,0.00081511104,0.000030501684,0.0000075025905,0.000013653066,0.0015199304,0.000042455482,0.001574574],"genre_scores_gemma":[0.99394965,0.0010993433,0.0014562863,0.00004524478,0.000012114015,0.000015540647,0.0027371047,0.000021788035,0.0006629382],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99958485,0.000020678768,0.00004896384,0.00015582953,0.00009428096,0.00009542397],"domain_scores_gemma":[0.99939716,0.000085042244,0.00015559683,0.000044123874,0.00013575099,0.00018232813],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00021409994,0.00030393392,0.00043044734,0.0023675505,0.0004477971,0.0006478167,0.00016610086,0.0002692498,0.00078456796],"category_scores_gemma":[0.00056711864,0.00020529563,0.0002930829,0.0010906039,0.00031232001,0.0004163115,0.0007356931,0.00022829806,0.00041515307],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00029221873,0.00002449561,0.11837639,0.00020314558,0.000064040905,0.00022047921,0.0005642788,0.00016256204,0.86886084,0.00022022788,0.000112091286,0.010899295],"study_design_scores_gemma":[0.000010023536,0.00018018507,0.9392991,0.00003667237,0.00007732182,0.0012889343,0.0005518003,0.0006955003,0.05358523,0.00027389816,0.0039635673,0.00003777947],"about_ca_topic_score_codex":0.0011135256,"about_ca_topic_score_gemma":0.0014995615,"teacher_disagreement_score":0.0023675505,"about_ca_system_score_codex":0.0002712826,"about_ca_system_score_gemma":0.000380974,"threshold_uncertainty_score":0.0026246905},"labels":[],"label_agreement":null},{"id":"W3132660211","doi":"10.1099/mgen.0.000510","title":"Comparative genomics of ST5 and ST30 methicillin-resistant Staphylococcus aureus sequential isolates recovered from paediatric patients with cystic fibrosis","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antimicrobial Resistance in Staphylococcus","field":"Medicine","cited_by":7,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Manitoba; Public Health Agency of Canada","funders":"Natural Sciences and Engineering Research Council of Canada; Secretaría de Ciencia y Técnica, Universidad de Buenos Aires; Universidad de Buenos Aires; Agencia Nacional de Promoción Científica y Tecnológica; Consejo Nacional de Investigaciones Científicas y Técnicas; Secretaria de Ciencia y Tecnica, Universidad de Buenos Aires; Public Health Agency; Public Health Agency of Canada","keywords":"Staphylococcus aureus; Virulence; Biology; Microbiology; Antibiotic resistance; Pathogen; Antimicrobial; Drug resistance; Human pathogen; Virology; Cystic fibrosis; Methicillin-resistant Staphylococcus aureus; Gene; Antibiotics; Genetics; Bacteria","score_opus":0.016646191817197037,"score_gpt":0.2451660400986866,"score_spread":0.22851984828148955,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3132660211","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9994642,0.000121688994,0.00010754595,0.000010756374,0.0000015010557,0.000003986541,0.00018772112,0.0000015581502,0.00010104481],"genre_scores_gemma":[0.99881554,0.000120748606,0.00033010123,0.000022107033,0.000004076008,0.000006209618,0.000598773,0.000003988987,0.000098535216],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99980694,0.000025989004,0.000018970944,0.00005709367,0.000047527355,0.000043483145],"domain_scores_gemma":[0.99968123,0.00007234063,0.00012864504,0.00001680212,0.00003617467,0.00006486563],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001168859,0.0002053567,0.00030803896,0.0005462627,0.00022465509,0.00027019615,0.00010377116,0.00026819628,0.000683677],"category_scores_gemma":[0.0006126066,0.00010706639,0.00028570936,0.0006163809,0.00020941654,0.00011654489,0.00026972822,0.00026149928,0.00013051629],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0008654343,0.0000839622,0.49385256,0.0001770594,0.000115095805,0.0042675124,0.0026020424,0.0003910284,0.48314002,0.00016190775,0.00028592141,0.0140575105],"study_design_scores_gemma":[0.000009170395,0.0002853202,0.9878626,0.000013273575,0.00003406465,0.003954026,0.0006040747,0.0002628385,0.006079854,0.000025360654,0.0008634258,0.0000060269704],"about_ca_topic_score_codex":0.0022751486,"about_ca_topic_score_gemma":0.0020733203,"teacher_disagreement_score":0.0022751486,"about_ca_system_score_codex":0.00017895526,"about_ca_system_score_gemma":0.00017953414,"threshold_uncertainty_score":0.0045238733},"labels":[],"label_agreement":null},{"id":"W3154460093","doi":"10.1099/mgen.0.000558","title":"Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Climate change and permafrost","field":"Earth and Planetary Sciences","cited_by":26,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Génome Québec; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Science Foundation","keywords":"Permafrost; Metagenomics; Functional diversity; Ecology; Diversity (politics); Shotgun; Geography; Geology; Biology; Gene","score_opus":0.04766053275584797,"score_gpt":0.21923695384665273,"score_spread":0.17157642109080476,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3154460093","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9985948,0.00022302142,0.00015379343,0.000008166805,0.0000014688416,0.0000036664649,0.00083761546,0.0000072097514,0.0001703821],"genre_scores_gemma":[0.99639916,0.00017641604,0.00040533431,0.000018171646,0.0000042330576,0.000011191148,0.0026618522,0.0000069861712,0.00031666792],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99983513,0.00000963086,0.000006158591,0.000071159295,0.000039215312,0.000038655337],"domain_scores_gemma":[0.9999106,0.0000116076335,0.000022852308,0.0000055425503,0.000025608068,0.00002368095],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00015286625,0.00051982014,0.00038946237,0.0010232097,0.00057541736,0.0006721427,0.00020068281,0.00037554384,0.0005667971],"category_scores_gemma":[0.00013100293,0.00016994515,0.00042920254,0.0007703119,0.00030832397,0.00026207787,0.00047564867,0.0002529508,0.00014479403],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000853502,0.00007877326,0.33809906,0.00020578169,0.00026273483,0.00033800467,0.0013403827,0.0007067906,0.6428147,0.000100850295,0.00017263202,0.015026805],"study_design_scores_gemma":[0.0000031289098,0.000054926837,0.99622285,0.0000070339606,0.000026520434,0.000079372636,0.0003340448,0.00032927672,0.002526933,0.00001261071,0.00039827818,0.0000049419727],"about_ca_topic_score_codex":0.0143334055,"about_ca_topic_score_gemma":0.016458748,"teacher_disagreement_score":0.0143334055,"about_ca_system_score_codex":0.00037372188,"about_ca_system_score_gemma":0.00028551114,"threshold_uncertainty_score":0.02849996},"labels":[],"label_agreement":null},{"id":"W3155636387","doi":"10.1099/mgen.0.000561","title":"Evaluation of bat adenoviruses suggests co-evolution and host roosting behaviour as drivers for diversity","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Virus-based gene therapy research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":17,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Ministry of Environment","funders":"Fogarty International Center; National Institutes of Health; Vancouver Island University; United States Agency for International Development; Foundation for the National Institutes of Health","keywords":"Biology; Host (biology); Phylogenetic tree; Zoology; Genetic diversity; Evolutionary biology; Ecology; Genetics; Gene","score_opus":0.03558518701686894,"score_gpt":0.31541381053713113,"score_spread":0.27982862352026217,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3155636387","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99878436,0.00040972666,0.00030766422,0.000014533561,0.000003764863,0.000008570484,0.00014415558,0.000004463213,0.00032272248],"genre_scores_gemma":[0.99943453,0.00008366992,0.00022841788,0.000006974784,0.0000040226646,0.0000045308548,0.00011568216,0.000002249422,0.00011987448],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99904794,0.0003012812,0.00006607586,0.00028000475,0.00012479085,0.00017986959],"domain_scores_gemma":[0.99753225,0.00095532346,0.0007801057,0.00014241507,0.00030825706,0.00028169775],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0012067661,0.00040962035,0.0004531747,0.0016334358,0.00046120695,0.001067824,0.00027127226,0.00037079342,0.0014998436],"category_scores_gemma":[0.002236113,0.00023472995,0.00037764135,0.000977025,0.0005615561,0.0007812313,0.00045920105,0.00045696864,0.00021672252],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0001302629,0.00001968629,0.98662853,0.000035796205,0.000046248868,0.00009407194,0.00028269654,0.00008930291,0.0105607025,0.0000577865,0.000016859913,0.0020379818],"study_design_scores_gemma":[0.0000010276001,0.00007805962,0.9984199,0.0000060250036,0.00002098235,0.00020688525,0.0003150309,0.00032997987,0.0004627167,0.000037976955,0.00011715534,0.0000042283873],"about_ca_topic_score_codex":0.002354507,"about_ca_topic_score_gemma":0.0025940384,"teacher_disagreement_score":0.002354507,"about_ca_system_score_codex":0.0003892007,"about_ca_system_score_gemma":0.00023093128,"threshold_uncertainty_score":0.0063821077},"labels":[],"label_agreement":null},{"id":"W3157723345","doi":"10.1099/mgen.0.000592","title":"Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":37,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Biotechnology and Biological Sciences Research Council; Medical Research Council; Imperial College Healthcare NHS Trust; Imperial College London; Trent University; Imperial Health Charity; Wellcome Trust; Nottingham Trent University","keywords":"Klebsiella oxytoca; Klebsiella; Biology; Genome; Microbiology; Gene; Genetics; Gene cluster; Phylogenetic tree; Locus (genetics); Sequence analysis; Klebsiella pneumoniae; Escherichia coli","score_opus":0.008639619264128717,"score_gpt":0.20174491950674878,"score_spread":0.19310530024262007,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3157723345","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99595636,0.0002505663,0.0020038434,0.00004384709,0.00000290789,0.00001853443,0.001290158,0.000025147396,0.000408687],"genre_scores_gemma":[0.98372686,0.00035789178,0.0075644725,0.000034528035,0.000007203577,0.000024439065,0.00750684,0.000024863659,0.00075285055],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9997756,0.00002456913,0.000034213157,0.000060543403,0.000065260014,0.000039750266],"domain_scores_gemma":[0.99968433,0.000054686512,0.00009826661,0.000039957762,0.00008316953,0.000039485425],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00016791256,0.00031214408,0.00030599063,0.0006161263,0.00019453267,0.00037776626,0.00022301922,0.0002740925,0.0007527568],"category_scores_gemma":[0.0007211459,0.00012224521,0.00026774232,0.0006288772,0.0001238777,0.00024405404,0.00030797024,0.00030711817,0.0003955878],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000081737904,0.000020898187,0.020185033,0.000048013262,0.0000135810715,0.00008043837,0.00011443571,0.00008097066,0.9769537,0.000024234487,0.00003226998,0.0023646741],"study_design_scores_gemma":[0.000010244241,0.00030716174,0.7090545,0.000030172538,0.000076146935,0.0016437224,0.0005337854,0.0024290162,0.2811307,0.00009793053,0.0046640425,0.000022482003],"about_ca_topic_score_codex":0.005150057,"about_ca_topic_score_gemma":0.0074389908,"teacher_disagreement_score":0.005150057,"about_ca_system_score_codex":0.0002208922,"about_ca_system_score_gemma":0.00020374008,"threshold_uncertainty_score":0.010240138},"labels":[],"label_agreement":null},{"id":"W3175871955","doi":"10.1099/mgen.0.000607","title":"SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":25,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University","funders":"European and Developing Countries Clinical Trials Partnership; Medical Research Council; Canadian Statistical Sciences Institute; European Commission; Natural Sciences and Engineering Research Council of Canada; Alfred P. Sloan Foundation; Foreign, Commonwealth and Development Office; Genome Canada","keywords":"Mycobacterium tuberculosis; Tuberculosis; Whole genome sequencing; Computational biology; Data science; Realm; Biology; Public health; Mycobacterium tuberculosis complex; Genome; Microbiology; Computer science; Medicine; Genetics; Geography; Gene","score_opus":0.035645701034219233,"score_gpt":0.3244036412700992,"score_spread":0.28875794023588,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3175871955","genre_codex":"methods","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":"methods","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.07684273,0.00053074094,0.8754885,0.0004951968,0.00027794956,0.00030425252,0.010830755,0.0331392,0.0020906862],"genre_scores_gemma":[0.21260698,0.00029871293,0.757757,0.00048026402,0.00017043173,0.0006440497,0.020036161,0.005829315,0.0021770725],"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.99733055,0.00096481893,0.0002821607,0.0008076758,0.0004611015,0.00015377726],"domain_scores_gemma":[0.9896337,0.0068026213,0.0012807786,0.0014070245,0.0005273851,0.0003485839],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.008019452,0.0014375008,0.0009803398,0.0052629136,0.0013105733,0.0024092933,0.0014814248,0.0015258684,0.005924739],"category_scores_gemma":[0.026905417,0.0008735899,0.0022074443,0.0024597978,0.0011562884,0.002243568,0.003104197,0.0020678313,0.0026340468],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0027067214,0.00059191394,0.13486928,0.0019618021,0.0040334724,0.0026711158,0.005104192,0.043089714,0.08184369,0.026255358,0.06929767,0.62757504],"study_design_scores_gemma":[0.0004349166,0.0005903245,0.049612287,0.00029108697,0.00056216837,0.0023506212,0.0018821367,0.6980208,0.05609296,0.102261566,0.08750521,0.0003958756],"about_ca_topic_score_codex":0.0016879966,"about_ca_topic_score_gemma":0.0031958488,"teacher_disagreement_score":0.008019452,"about_ca_system_score_codex":0.00049115624,"about_ca_system_score_gemma":0.0013365753,"threshold_uncertainty_score":0.042411387},"labels":[],"label_agreement":null},{"id":"W3177970688","doi":"10.1099/mgen.0.000597","title":"RETRACTED: Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Milk Quality and Mastitis in Dairy Cows","field":"Agricultural and Biological Sciences","cited_by":21,"is_retracted":true,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal; Health Canada; Fonds de Recherche du Québec – Nature et Technologies; McGill University; Cegep de Saint Hyacinthe","funders":"Dairy Farmers of Canada","keywords":"Biology; Escherichia coli; Bacterial adhesin; Microbiology; Gene; Mastitis; Major facilitator superfamily; Virulence; Genetics; Transporter","score_opus":0.06437888419482884,"score_gpt":0.28174622635965674,"score_spread":0.2173673421648279,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3177970688","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9137772,0.010950997,0.006491788,0.01591951,0.023276882,0.00017643638,0.011349933,0.00054401584,0.017513229],"genre_scores_gemma":[0.92031777,0.008070545,0.011467156,0.004173899,0.004115776,0.00009075125,0.017439628,0.00039423254,0.03393018],"study_design_codex":"design_other","study_design_gemma":"observational","domain_scores_codex":[0.99916935,0.000110576424,0.00014211026,0.0001302864,0.00034460012,0.00010308911],"domain_scores_gemma":[0.997647,0.0009240316,0.00041543887,0.00026484125,0.00054406124,0.00020456956],"candidate_categories":["research_integrity"],"consensus_categories":[],"category_scores_codex":[0.00049780245,0.00058119325,0.00036100193,0.0012459091,0.00073620013,0.0011744888,0.0009358525,0.0017579525,0.008127368],"category_scores_gemma":[0.0050689243,0.00020034042,0.0004519773,0.0017023725,0.0006231222,0.0005735445,0.00069552206,0.0012912964,0.0045907884],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0022006342,0.0003771266,0.14847092,0.0025041464,0.00026558363,0.09350229,0.0058463905,0.0007314982,0.2622809,0.0020336872,0.16601378,0.3157732],"study_design_scores_gemma":[0.00007821949,0.0006671846,0.46934947,0.00069444673,0.00025729788,0.10318377,0.0039007687,0.0013262832,0.045863777,0.00054457714,0.3740287,0.0001054058],"about_ca_topic_score_codex":0.0026159037,"about_ca_topic_score_gemma":0.0015834,"teacher_disagreement_score":0.998242,"about_ca_system_score_codex":0.00054427446,"about_ca_system_score_gemma":0.00050641433,"threshold_uncertainty_score":0.027188718},"labels":[],"label_agreement":null},{"id":"W3181464471","doi":"10.1099/mgen.0.000585","title":"Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Plant Pathogenic Bacteria Studies","field":"Agricultural and Biological Sciences","cited_by":9,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada; Erciyes Üniversitesi","keywords":"Biology; Pseudomonas syringae; Virulence; Pseudomonas fluorescens; Pathovar; Comparative genomics; Microbiology; Pseudomonas; Botany; Genetics; Bacteria; Pseudomonadaceae; Genome; Genomics; Gene; Pathogen","score_opus":0.03334127407514395,"score_gpt":0.22419076122400175,"score_spread":0.1908494871488578,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3181464471","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9978276,0.00033364387,0.00047940336,0.000019072022,0.0000045091365,0.00001335189,0.00082933425,0.000012563891,0.0004805929],"genre_scores_gemma":[0.99472976,0.00030435153,0.001264693,0.00004207036,0.0000048147845,0.000013353438,0.0033293176,0.000010418667,0.00030102153],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9997757,0.000019878671,0.000020599879,0.00008433692,0.00003673657,0.00006274683],"domain_scores_gemma":[0.99977773,0.000033247456,0.00008898805,0.0000122958245,0.000042839198,0.000044912907],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000127676,0.00040214215,0.00029757718,0.001563881,0.0001898819,0.0003268191,0.0002282445,0.0003405324,0.0006006091],"category_scores_gemma":[0.0002946016,0.000201331,0.0004413707,0.0010437499,0.00018327533,0.0001744653,0.00033163253,0.00034696373,0.00024077439],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0008696723,0.00010412372,0.07771132,0.00021956615,0.00008699771,0.0008539867,0.00067079294,0.000527608,0.90477824,0.00016950745,0.00017270043,0.013835529],"study_design_scores_gemma":[0.00001544987,0.00037492343,0.97851473,0.000027810427,0.00008945404,0.0017481954,0.00069376285,0.00066015066,0.0156853,0.00006702137,0.0021078696,0.000015415768],"about_ca_topic_score_codex":0.0031575328,"about_ca_topic_score_gemma":0.003317067,"teacher_disagreement_score":0.0031575328,"about_ca_system_score_codex":0.00043631427,"about_ca_system_score_gemma":0.00022767461,"threshold_uncertainty_score":0.0062782764},"labels":[],"label_agreement":null},{"id":"W3188833741","doi":"10.1099/mgen.0.000639","title":"Association between metabolic status and gut microbiome in obese populations","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Dalhousie University","funders":"National Key Clinical Specialty Discipline Construction Program of China; Chinese People’s Liberation Army; Southwest Hospital; Sanming Project of Medicine in Shenzhen; National Natural Science Foundation of China","keywords":"Gut microbiome; Association (psychology); Microbiome; Obesity; Biology; Medicine; Internal medicine; Genetics; Psychology","score_opus":0.01578785445639869,"score_gpt":0.26581934942444296,"score_spread":0.2500314949680443,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3188833741","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9996232,0.0001075728,0.00005071319,0.00001568988,0.0000016177306,0.0000017796581,0.000060869297,7.590825e-7,0.0001377492],"genre_scores_gemma":[0.9997116,0.000056293164,0.00006811889,0.0000134334905,0.0000026077523,0.000002312774,0.000075808406,9.810074e-7,0.00006878239],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9998271,0.000042380816,0.000015222619,0.000045844743,0.000029498478,0.000040045303],"domain_scores_gemma":[0.9996953,0.000037216487,0.0001467296,0.000027275568,0.000028940698,0.0000645858],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00037346722,0.00019869943,0.00019346498,0.00065907266,0.00034204914,0.00037600918,0.00010225079,0.00023582937,0.0010085222],"category_scores_gemma":[0.0008826913,0.00013102617,0.00018533174,0.0005593557,0.00019970514,0.00018174342,0.0004206103,0.00022301453,0.00005795759],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00019187648,0.000016165533,0.99483114,0.0000091497695,0.000050022383,0.000045967383,0.00008907272,0.00002689736,0.0029469868,0.000024300665,0.000024470877,0.0017440198],"study_design_scores_gemma":[0.0000013776682,0.000021285112,0.9997149,0.0000016496189,0.000007683672,0.0000418753,0.000059103048,0.00004784294,0.000050987244,0.000014185826,0.00003801407,0.0000010158559],"about_ca_topic_score_codex":0.004600178,"about_ca_topic_score_gemma":0.006173788,"teacher_disagreement_score":0.004600178,"about_ca_system_score_codex":0.00018010235,"about_ca_system_score_gemma":0.00013141932,"threshold_uncertainty_score":0.00914681},"labels":[],"label_agreement":null},{"id":"W3195484595","doi":"10.1099/mgen.0.000625","title":"Shining light on a deep-sea bacterial symbiont population structure with CRISPR","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":8,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Victoria; Université de Montréal","funders":"Natural Sciences and Engineering Research Council of Canada; Natural Environment Research Council; Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada; Sight Research UK; Compute Canada","keywords":"Biology; CRISPR; Population; Evolutionary biology; Genetic diversity; Phylogenetic tree; Locus (genetics); Symbiotic bacteria; Genetics; Ecology; Gene; Bacteria; Symbiosis","score_opus":0.005480703860007935,"score_gpt":0.1945221730154995,"score_spread":0.18904146915549158,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3195484595","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9705893,0.001241197,0.025806785,0.000383667,0.000021691496,0.000013878055,0.00045596095,0.00016189719,0.0013255733],"genre_scores_gemma":[0.98670805,0.000519529,0.011853826,0.00015003674,0.000013005063,0.000019590147,0.00019025823,0.000021679147,0.0005239614],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9996346,0.00006029944,0.000026476335,0.00014637239,0.00008214327,0.000050143593],"domain_scores_gemma":[0.9991115,0.0002844377,0.0002733739,0.00015043475,0.00008853999,0.000091749374],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005329509,0.00027755473,0.0003877455,0.00049862,0.00024086461,0.00067224714,0.00048438367,0.0004702792,0.000769404],"category_scores_gemma":[0.0010490598,0.00021711175,0.00028741063,0.00053911516,0.0005916517,0.0007288758,0.0007684211,0.000848791,0.00013995933],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00016172172,0.00006187363,0.080517046,0.00029424398,0.00015426679,0.00025071824,0.0009376736,0.0029227496,0.8560275,0.0021161225,0.0002860822,0.0562699],"study_design_scores_gemma":[0.000028011975,0.0008543235,0.68137866,0.0001438286,0.00024794514,0.0013428935,0.002577323,0.024995971,0.2639995,0.009473244,0.014822618,0.00013573024],"about_ca_topic_score_codex":0.0010046082,"about_ca_topic_score_gemma":0.002347295,"teacher_disagreement_score":0.0010046082,"about_ca_system_score_codex":0.00036844015,"about_ca_system_score_gemma":0.00025794294,"threshold_uncertainty_score":0.0028185844},"labels":[],"label_agreement":null},{"id":"W3195733379","doi":"10.1099/mgen.0.000613","title":"Genomic insights into the diversity, virulence and resistance of Klebsiella pneumoniae extensively drug resistant clinical isolates","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":20,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University; University of British Columbia","funders":"Simon Fraser University; Killam Trusts; Conselho Nacional de Desenvolvimento Científico e Tecnológico; Michael Smith Health Research BC; Canadian Institutes of Health Research; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Fundação de Apoio à Pesquisa do Distrito Federal; Wellcome Trust","keywords":"Klebsiella pneumoniae; Biology; Drug resistance; Virulence; Microbiology; Multiple drug resistance; Gene; Genome; Efflux; Antibiotic resistance; Antibiotics; Whole genome sequencing; Clade; Genetics; Escherichia coli; Phylogenetics","score_opus":0.011158805787706763,"score_gpt":0.23978500930987046,"score_spread":0.2286262035221637,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3195733379","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9892775,0.0021788368,0.0017974076,0.00016584982,0.00000973438,0.00002279936,0.0050097955,0.00003192992,0.0015061382],"genre_scores_gemma":[0.9906895,0.0013962161,0.002621743,0.00009980919,0.000011837424,0.000015079643,0.0047600367,0.000017352855,0.00038839097],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99978036,0.000026147167,0.000021487038,0.00007892336,0.000048225793,0.000044827102],"domain_scores_gemma":[0.99969053,0.00006987421,0.000104489445,0.000025813768,0.00006400886,0.00004528367],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001604638,0.00030296706,0.0002876982,0.0014371031,0.00023426198,0.00051550445,0.00013163128,0.00030454854,0.00067599455],"category_scores_gemma":[0.0007485278,0.00015078348,0.00036872405,0.0014725646,0.00021222868,0.00024830276,0.0003139563,0.0003048812,0.0002953736],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00035039338,0.00006490892,0.14170504,0.00039558765,0.000090245085,0.00086418877,0.001272993,0.0005672915,0.82887363,0.0003503471,0.0003718787,0.02509358],"study_design_scores_gemma":[0.0000103650345,0.00016274244,0.9648446,0.00009091846,0.0001302338,0.0021362132,0.001108295,0.0011263506,0.02157515,0.0003319366,0.008459248,0.000023893235],"about_ca_topic_score_codex":0.0049367086,"about_ca_topic_score_gemma":0.0071032485,"teacher_disagreement_score":0.0049367086,"about_ca_system_score_codex":0.0002916074,"about_ca_system_score_gemma":0.00040979788,"threshold_uncertainty_score":0.009815931},"labels":[],"label_agreement":null},{"id":"W3196015129","doi":"10.1099/mgen.0.000620","title":"Evolution and emergence of multidrug-resistant Mycobacterium tuberculosis in Chisinau, Moldova","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Tuberculosis Research and Epidemiology","field":"Medicine","cited_by":15,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University","funders":"National Center for Advancing Translational Sciences; National Institute of Allergy and Infectious Diseases","keywords":"Tuberculosis; Mycobacterium tuberculosis; Population; Public health; Drug resistance; Mycobacterium tuberculosis complex; Biology; Evolutionary biology; Medicine; Genetics; Environmental health; Pathology","score_opus":0.016016660580519534,"score_gpt":0.27561566264204973,"score_spread":0.2595990020615302,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3196015129","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9994948,0.00016011074,0.000058631984,0.000030139106,0.0000027331112,0.0000028618567,0.00002857887,0.0000030815474,0.00021895397],"genre_scores_gemma":[0.99965334,0.00009658775,0.00011117203,0.000014910542,0.0000021957526,0.00000243072,0.00006274407,0.0000021036692,0.0000545212],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99974674,0.000046223995,0.000012890653,0.000083814826,0.000016804855,0.0000935368],"domain_scores_gemma":[0.9997558,0.000038820468,0.00010890584,0.000024852941,0.000019414221,0.00005218228],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004240347,0.00035181976,0.00029601413,0.0014646874,0.0009885837,0.0011247814,0.00042660782,0.00042529593,0.00038384722],"category_scores_gemma":[0.00087425153,0.00023056476,0.00026961975,0.0011662663,0.0010210337,0.00040113786,0.0010027445,0.00047295223,0.00007865811],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00029988008,0.00004825149,0.9590542,0.000039702485,0.00007909303,0.0014264904,0.0032537288,0.0012592378,0.015452904,0.0008233599,0.00010669797,0.018156473],"study_design_scores_gemma":[0.0000063075727,0.00003779105,0.9976197,0.000017873577,0.00001111994,0.00020887773,0.0006816295,0.0005309197,0.00031435033,0.00008456438,0.00047943127,0.000007445147],"about_ca_topic_score_codex":0.023494149,"about_ca_topic_score_gemma":0.040449824,"teacher_disagreement_score":0.023494149,"about_ca_system_score_codex":0.0014132519,"about_ca_system_score_gemma":0.00070778944,"threshold_uncertainty_score":0.046714783},"labels":[],"label_agreement":null},{"id":"W3200050118","doi":"10.1099/mgen.0.000651","title":"Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Canadian Food Inspection Agency; University of Manitoba; Public Health Agency of Canada","funders":"","keywords":"Genotyping; Computational biology; SNP; Genome; Biology; SNP genotyping; Whole genome sequencing; Population; Genetics; Genotype; Single-nucleotide polymorphism; Gene; Medicine","score_opus":0.013422860833165464,"score_gpt":0.2086689526788758,"score_spread":0.19524609184571035,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3200050118","genre_codex":"methods","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":"methods","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.41655678,0.001396122,0.5141013,0.00047423394,0.00031798278,0.00051698927,0.016742043,0.039531257,0.010363285],"genre_scores_gemma":[0.2222649,0.00031450723,0.7603756,0.00031440644,0.000040408817,0.00058441516,0.009563225,0.0011444726,0.005398139],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9968863,0.0006827621,0.00027548277,0.0010585199,0.0008907955,0.00020612057],"domain_scores_gemma":[0.99593395,0.001761535,0.00084739336,0.00088480767,0.0004310954,0.00014126915],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002624643,0.00079497736,0.00083515677,0.0020417813,0.0005988646,0.0016938872,0.0012071105,0.001198991,0.004503185],"category_scores_gemma":[0.004748385,0.0006695087,0.00080675835,0.0015153995,0.00062964245,0.0011756894,0.0015178084,0.00085191417,0.0037354345],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0018821736,0.0003033502,0.033941224,0.0009830934,0.00037524774,0.0004895033,0.0011174883,0.01740883,0.65893286,0.005610417,0.013134536,0.26582128],"study_design_scores_gemma":[0.00014623896,0.00060111925,0.04835206,0.00013474259,0.00018428986,0.0010342138,0.00039583226,0.18243295,0.7172928,0.004118211,0.04490479,0.00040278412],"about_ca_topic_score_codex":0.0011100676,"about_ca_topic_score_gemma":0.003197566,"teacher_disagreement_score":0.004503185,"about_ca_system_score_codex":0.00046974584,"about_ca_system_score_gemma":0.0007659143,"threshold_uncertainty_score":0.015064657},"labels":[],"label_agreement":null},{"id":"W3209352051","doi":"10.1099/mgen.0.000672","title":"Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Centre Intégré Universitaire de Santé et de Services Sociaux du Centre-Sud-de-l'Île-de-Montréal; Université de Montréal; Centre Hospitalier de l’Université de Montréal; Ste. Anne's Hospital","funders":"","keywords":"Subtyping; Outbreak; Multilocus sequence typing; Shigella sonnei; Biology; Whole genome sequencing; Genetics; Shigellosis; Typing; Shigella; Genome; Virology; Genotype; Salmonella; Gene; Computer science","score_opus":0.02495348164995905,"score_gpt":0.3585431468141583,"score_spread":0.33358966516419924,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3209352051","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9831709,0.0018960449,0.013689514,0.000103173064,0.00001703529,0.00014298748,0.00029514413,0.000050710267,0.0006345264],"genre_scores_gemma":[0.9586823,0.0010811362,0.0386631,0.000056602556,0.000016926813,0.00011053996,0.00093620684,0.000025149999,0.00042795113],"study_design_codex":"observational","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9863105,0.00745755,0.0009150331,0.0013688804,0.0036365043,0.00031161273],"domain_scores_gemma":[0.9777159,0.0143752545,0.0023235346,0.0012196396,0.003674783,0.00069093663],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.018306335,0.0010452035,0.00069806667,0.002697183,0.00035686977,0.0009395437,0.000977166,0.0007425149,0.00034662732],"category_scores_gemma":[0.017727578,0.00035584802,0.00071028783,0.0014864702,0.0007033314,0.00087901135,0.000936488,0.0005898018,0.00014822057],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.01020347,0.0019921968,0.43812227,0.0013094409,0.0010841974,0.00029691216,0.0019222753,0.017993348,0.31981862,0.00045221014,0.00040961534,0.2063954],"study_design_scores_gemma":[0.0003104265,0.02549652,0.6480936,0.00021867605,0.00081390014,0.0011116943,0.0008081388,0.10275865,0.2169985,0.0003511302,0.0028054595,0.00023344385],"about_ca_topic_score_codex":0.0023073184,"about_ca_topic_score_gemma":0.0042028064,"teacher_disagreement_score":0.018306335,"about_ca_system_score_codex":0.00055995636,"about_ca_system_score_gemma":0.00080459367,"threshold_uncertainty_score":0.096814275},"labels":[],"label_agreement":null},{"id":"W3215832582","doi":"10.1099/mgen.0.000728","title":"ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":131,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Canadian Food Inspection Agency; Public Health Agency of Canada","funders":"Public Health Agency of Canada","keywords":"In silico; Serotype; Escherichia coli; Whole genome sequencing; Computational biology; Genome; Sequence (biology); Biology; Genetics; Raw data; Microbiology; Gene; Mathematics; Statistics","score_opus":0.03759364213199561,"score_gpt":0.26970089921755236,"score_spread":0.23210725708555674,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3215832582","genre_codex":"empirical","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.529359,0.0015749775,0.25782013,0.0005688648,0.0005291073,0.00067174685,0.11154701,0.09127221,0.0066569825],"genre_scores_gemma":[0.39795214,0.0005754066,0.38595167,0.0005128276,0.00008125177,0.0005740407,0.20660265,0.0055635045,0.0021864844],"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9983631,0.0004732275,0.00017992225,0.0005479712,0.00029946188,0.00013638404],"domain_scores_gemma":[0.99822503,0.0010007693,0.0001562412,0.0002871705,0.00024256368,0.000088327055],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0033718226,0.0026324387,0.001150499,0.0017824525,0.00052426744,0.0015850102,0.0013606313,0.0009355057,0.0033909096],"category_scores_gemma":[0.006593344,0.0007955601,0.0025431365,0.001063898,0.00030940346,0.00089569204,0.0013331103,0.0013285468,0.0031456503],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00585791,0.0012775492,0.19468358,0.00578902,0.0037996536,0.002735483,0.0016004256,0.25177273,0.20281632,0.005023296,0.119748525,0.20489556],"study_design_scores_gemma":[0.00037150548,0.0008424328,0.038373288,0.00030419842,0.00044704764,0.0010239064,0.0004881643,0.8276818,0.08285506,0.004808929,0.042584646,0.00021903549],"about_ca_topic_score_codex":0.0030194246,"about_ca_topic_score_gemma":0.0052474616,"teacher_disagreement_score":0.0033909096,"about_ca_system_score_codex":0.00044263154,"about_ca_system_score_gemma":0.0013065826,"threshold_uncertainty_score":0.0178321},"labels":[],"label_agreement":null},{"id":"W3216102782","doi":"10.1099/mgen.0.000687","title":"Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405: comparative analysis with draft genomes for different laboratory stock cultures indicates little genetic variation","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial infections and disease research","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal","funders":"Biotechnology and Biological Sciences Research Council; Directorate for Biological Sciences; National Natural Science Foundation of China; Wellcome Trust; Royal Veterinary College; Zoetis; London School of Hygiene and Tropical Medicine; Imperial College London; Pfizer","keywords":"Biology; Whole genome sequencing; Genome; Genetics; Reference genome; Actinobacillus pleuropneumoniae; DNA sequencing; Computational biology; Gene","score_opus":0.03569766944689609,"score_gpt":0.28868343881081787,"score_spread":0.2529857693639218,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3216102782","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.872376,0.0022921397,0.02127784,0.00030956737,0.00015483766,0.00016047711,0.0969719,0.0007622351,0.0056949914],"genre_scores_gemma":[0.4955753,0.0022840798,0.04722014,0.00020853714,0.000047839327,0.00031869626,0.4492543,0.00058805064,0.004502918],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9995833,0.00003351647,0.00003928343,0.00011667735,0.00017767739,0.000049467853],"domain_scores_gemma":[0.999488,0.000083276995,0.000117757656,0.00008070213,0.00017622158,0.000054110977],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00054713653,0.00077242154,0.0005250471,0.0011886135,0.0003836374,0.00072388526,0.00054924143,0.0005299081,0.0025187284],"category_scores_gemma":[0.0013010089,0.0002351468,0.00049233815,0.0018493191,0.00020267964,0.00047723114,0.00047266876,0.0006254805,0.0016559054],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0011877673,0.00011295911,0.011081043,0.0008697664,0.00009473852,0.00035712778,0.00040024536,0.00080385676,0.9481953,0.00041937953,0.002796366,0.033681452],"study_design_scores_gemma":[0.00022087498,0.0018229367,0.29875338,0.00054056116,0.00084455963,0.002388252,0.0014949383,0.0049130046,0.49893317,0.0010145908,0.18890908,0.00016455083],"about_ca_topic_score_codex":0.003621646,"about_ca_topic_score_gemma":0.0038751205,"teacher_disagreement_score":0.003621646,"about_ca_system_score_codex":0.0005306261,"about_ca_system_score_gemma":0.000819262,"threshold_uncertainty_score":0.008426011},"labels":[],"label_agreement":null},{"id":"W3217282564","doi":"10.1099/mgen.0.000681","title":"Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial biofilms and quorum sensing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université Laval","funders":"Canadian Institutes of Health Research; Health Research Council of New Zealand; Otago Medical Research Foundation; Cystic Fibrosis Canada","keywords":"Biology; Transcriptome; Pseudomonas aeruginosa; Phenotype; Gene; Genetics; Microbiology; Genome; Experimental evolution; Bacteria; Gene expression","score_opus":0.006253384314490761,"score_gpt":0.19114679985093933,"score_spread":0.18489341553644856,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W3217282564","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9981357,0.00046284712,0.0005637737,0.00006623744,0.0000053103704,0.0000054625934,0.00040062307,0.000012686807,0.00034727575],"genre_scores_gemma":[0.99754816,0.0003813518,0.00052885205,0.00012837838,0.000014015583,0.000021443911,0.0010450485,0.000013574551,0.0003191998],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9997621,0.000034942124,0.000013490441,0.00008235951,0.000053068405,0.000054050717],"domain_scores_gemma":[0.999587,0.00010211836,0.00014207778,0.0000276621,0.00007472507,0.00006650763],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00029336053,0.00016894231,0.0003552601,0.0004694318,0.00028257453,0.00054453337,0.0001712556,0.00056174106,0.00057126995],"category_scores_gemma":[0.000832874,0.00018775428,0.0002714464,0.0005155455,0.00028663976,0.00040983577,0.0005370867,0.00046723807,0.00020709216],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00031347183,0.000039316204,0.050077718,0.00007058812,0.00005444036,0.0005350531,0.00050718064,0.0003436995,0.9421113,0.00014563148,0.00009278129,0.005708776],"study_design_scores_gemma":[0.000005326033,0.0002529254,0.9739751,0.000016763399,0.000048042028,0.00086990104,0.0005775549,0.0011488362,0.020842977,0.00023478873,0.0020081943,0.000019677675],"about_ca_topic_score_codex":0.00063315977,"about_ca_topic_score_gemma":0.0007500273,"teacher_disagreement_score":0.00063315977,"about_ca_system_score_codex":0.00027152585,"about_ca_system_score_gemma":0.00014275982,"threshold_uncertainty_score":0.0019701123},"labels":[],"label_agreement":null},{"id":"W4200620572","doi":"10.1099/mgen.0.000713","title":"Mobility of β-lactam resistance under ampicillin treatment in gut microbiota suffering from pre-disturbance","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Public Health Agency of Canada; Agriculture and Agri-Food Canada; Canadian Food Inspection Agency","funders":"","keywords":"Ampicillin; Disturbance (geology); Resistance (ecology); Amp resistance; Lactam; Microbiology; Biology; Ecology; Antibiotics; Chemistry; Stereochemistry","score_opus":0.009657855147184263,"score_gpt":0.23231526382270498,"score_spread":0.22265740867552072,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4200620572","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99907863,0.00020199982,0.00024373404,0.00003132311,0.000014303461,0.000013418253,0.000096414915,0.0000129493155,0.0003072718],"genre_scores_gemma":[0.997127,0.00031775443,0.0006892255,0.00011778845,0.000013618264,0.000042023363,0.00042442174,0.000011602719,0.0012564964],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9997981,0.000025054684,0.000014618283,0.000051173054,0.000035167,0.000075818505],"domain_scores_gemma":[0.99975246,0.000015178287,0.00007028033,0.000016775713,0.000022211621,0.00012305233],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00010769828,0.0003496207,0.00035421478,0.00024430174,0.00017754678,0.0003346054,0.00011284342,0.00034199547,0.0011917753],"category_scores_gemma":[0.00023228607,0.0001797174,0.00032631878,0.00013714145,0.00026992915,0.0002240448,0.00036496008,0.00084705505,0.00023290634],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00074379164,0.00008728616,0.0020473837,0.000028716004,0.0000052690866,0.00013267968,0.000043018917,0.000016787255,0.9959253,0.000016852942,0.00002385347,0.0009291031],"study_design_scores_gemma":[0.000104934414,0.012873526,0.25779846,0.00004450068,0.00008669321,0.002650765,0.0007792041,0.001113919,0.72191876,0.00016775189,0.0024248643,0.00003663582],"about_ca_topic_score_codex":0.00028411215,"about_ca_topic_score_gemma":0.00035046396,"teacher_disagreement_score":0.0011917753,"about_ca_system_score_codex":0.00014420623,"about_ca_system_score_gemma":0.00016413818,"threshold_uncertainty_score":0.0039868355},"labels":[],"label_agreement":null},{"id":"W4212861999","doi":"10.1099/mgen.0.000779","title":"Comparative genomic analysis of Staphylococcus aureus isolates associated with either bovine intramammary infections or human infections demonstrates the importance of restriction-modification systems in host adaptation","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Milk Quality and Mastitis in Dairy Cows","field":"Agricultural and Biological Sciences","cited_by":22,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal; Université de Sherbrooke; McGill University; Fonds de Recherche du Québec – Nature et Technologies; Cegep de Saint Hyacinthe","funders":"","keywords":"Staphylococcus aureus; Mastitis; Biology; Microbiology; Virulence; Staphylococcal infections; Host adaptation; Gene; Genetics; Bacteria","score_opus":0.04085967212749763,"score_gpt":0.25813859743651413,"score_spread":0.2172789253090165,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4212861999","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.996073,0.0010499322,0.0007959271,0.00003460445,0.0000061766427,0.000011420275,0.0014037912,0.000009703277,0.00061540416],"genre_scores_gemma":[0.9953355,0.00046470837,0.001328807,0.000049698254,0.000005933618,0.000009242322,0.0025394403,0.0000053960703,0.000261238],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99980825,0.000020355596,0.000016532404,0.00006695847,0.00003993281,0.0000480071],"domain_scores_gemma":[0.999689,0.00006396006,0.00014203998,0.000021072972,0.000040014616,0.000043908793],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00013222631,0.00020369481,0.00022773998,0.00079834904,0.00019957988,0.00028128404,0.000084922314,0.00023044301,0.00092516537],"category_scores_gemma":[0.0003874538,0.000080864316,0.00028244173,0.0009276903,0.0001694846,0.00010473096,0.00022673812,0.00021058509,0.00021689203],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0005807469,0.00008228279,0.28603104,0.0002966069,0.00013050734,0.00083759736,0.0008415495,0.00019628595,0.69073594,0.00019099165,0.00025736986,0.019819004],"study_design_scores_gemma":[0.000005434023,0.00022706886,0.9771599,0.000035727153,0.00009607514,0.0021289065,0.00057470094,0.0004177204,0.016885143,0.000088937726,0.0023717068,0.000008733641],"about_ca_topic_score_codex":0.0024852785,"about_ca_topic_score_gemma":0.00339017,"teacher_disagreement_score":0.0024852785,"about_ca_system_score_codex":0.00013245181,"about_ca_system_score_gemma":0.00017135411,"threshold_uncertainty_score":0.0049416423},"labels":[],"label_agreement":null},{"id":"W4220861525","doi":"10.1099/mgen.0.000747","title":"regentrans: a framework and R package for using genomics to study regional pathogen transmission","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"National Human Genome Research Institute; National Institute of Allergy and Infectious Diseases; Canadian Institutes of Health Research; National Institutes of Health","keywords":"Transmission (telecommunications); Genome; Genomics; Computer science; Computational biology; Data science; Biology; Telecommunications; Genetics","score_opus":0.01876917729205897,"score_gpt":0.2624466408676545,"score_spread":0.24367746357559555,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4220861525","genre_codex":"methods","genre_gemma":"software","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"software","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.005984389,0.0016229254,0.5520876,0.0017748408,0.00076194934,0.0005735704,0.130049,0.30215645,0.004989184],"genre_scores_gemma":[0.05203392,0.002002195,0.66393226,0.0022165258,0.0003671692,0.0045159073,0.1149049,0.15503602,0.0049911183],"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9963909,0.0018051038,0.00032521551,0.00066814333,0.0006046317,0.00020610854],"domain_scores_gemma":[0.9840089,0.011849499,0.0011870333,0.0014229763,0.0010301329,0.0005014921],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.008888927,0.0036370473,0.0026823885,0.003192184,0.00074290956,0.0034183513,0.0043760994,0.0015222802,0.035085745],"category_scores_gemma":[0.043877326,0.0025566297,0.0039609284,0.002995045,0.0012911255,0.002184017,0.0042928993,0.0040753,0.026779944],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0011551704,0.00019464188,0.019852396,0.006465851,0.005284629,0.0013573837,0.001127852,0.043488417,0.0065304427,0.038284108,0.77273095,0.10352817],"study_design_scores_gemma":[0.0013382378,0.00032156523,0.012613312,0.0011265433,0.0013390338,0.0013176681,0.00031410207,0.14228533,0.009087195,0.10834359,0.7213988,0.0005146572],"about_ca_topic_score_codex":0.0056255683,"about_ca_topic_score_gemma":0.0067829676,"teacher_disagreement_score":0.035085745,"about_ca_system_score_codex":0.0010155917,"about_ca_system_score_gemma":0.004453322,"threshold_uncertainty_score":0.11737347},"labels":[],"label_agreement":null},{"id":"W4225330733","doi":"10.1099/mgen.0.000781","title":"An inventory of early branch points in microbial phosphonate biosynthesis","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Biochemical and Molecular Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Wilfrid Laurier University","funders":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","keywords":"Mutase; Biosynthesis; Phosphonate; Gene; Operon; Horizontal gene transfer; Biology; Enzyme; Biochemistry; Genome; Chemistry; Stereochemistry; Escherichia coli","score_opus":0.009271039816025431,"score_gpt":0.23413204364449255,"score_spread":0.22486100382846713,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4225330733","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9845893,0.0027456323,0.0047044675,0.000077971534,0.000014866205,0.000019746149,0.004741087,0.00039386415,0.002713043],"genre_scores_gemma":[0.94591457,0.00379003,0.017399024,0.00010361252,0.000022038295,0.00007231774,0.030102186,0.00030009766,0.0022961718],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99952424,0.00004480784,0.000027712986,0.00017705948,0.00013542155,0.00009069847],"domain_scores_gemma":[0.99948716,0.00016643673,0.000091606715,0.00005709408,0.00009859677,0.0000989771],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00031827224,0.0005510387,0.0007956041,0.0018176092,0.00059228163,0.0011462567,0.00043103984,0.0005808256,0.0022321758],"category_scores_gemma":[0.0012974772,0.00032750718,0.0013751319,0.0023930704,0.00035206936,0.0009904145,0.0008344973,0.0004674514,0.0012885039],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0020941636,0.0002780974,0.46490395,0.0024829728,0.0005253506,0.0011721856,0.000711308,0.06700648,0.30119792,0.0050994563,0.0047363695,0.14979176],"study_design_scores_gemma":[0.000121319084,0.0013657003,0.58264136,0.00037154095,0.0009909687,0.0030006508,0.0016356193,0.27270678,0.0712558,0.013665866,0.05200851,0.00023590784],"about_ca_topic_score_codex":0.0023871798,"about_ca_topic_score_gemma":0.0042504477,"teacher_disagreement_score":0.0023871798,"about_ca_system_score_codex":0.0004959246,"about_ca_system_score_gemma":0.0006998182,"threshold_uncertainty_score":0.0074673295},"labels":[],"label_agreement":null},{"id":"W4225725684","doi":"10.1099/mgen.0.000759","title":"Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacillus and Francisella bacterial research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"H2020 Marie Skłodowska-Curie Actions; Biotechnology and Biological Sciences Research Council; University of Glasgow; Directorate for Biological Sciences; Academy of Medical Sciences; Wellcome Trust; Natural Sciences and Engineering Research Council of Canada; Bill and Melinda Gates Foundation","keywords":"Bacillus anthracis; Biology; Transmission (telecommunications); Genetic diversity; Genomics; Genome; Genetics; Evolutionary biology; Population; Environmental health; Gene","score_opus":0.017092265453224197,"score_gpt":0.25757576479803096,"score_spread":0.24048349934480676,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4225725684","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9996549,0.00002334186,0.00014873207,0.00001402037,8.1647886e-7,0.0000017190056,0.00009973179,0.0000036691076,0.000053008593],"genre_scores_gemma":[0.9992353,0.000025717063,0.00026977676,0.000017276507,0.000001816582,0.0000035968087,0.0004001824,0.0000022798388,0.00004422836],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9997886,0.000054309774,0.000007681622,0.00009042281,0.000016220576,0.000042842403],"domain_scores_gemma":[0.99964476,0.00012231628,0.00009307356,0.000037517573,0.000046235637,0.00005606781],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005731452,0.00019480869,0.00019788642,0.0003915133,0.00037130385,0.00037043655,0.00021835841,0.00030282093,0.00074243813],"category_scores_gemma":[0.0009091175,0.00014395673,0.0002787965,0.00047817783,0.00032653412,0.00022902098,0.00033609188,0.0004113533,0.00010315444],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00041455813,0.00020662036,0.92262834,0.000062983156,0.0002015749,0.0004127888,0.0022059442,0.0065393383,0.05503003,0.00055518816,0.0006719731,0.011070593],"study_design_scores_gemma":[0.000015737083,0.000109017514,0.9914892,0.000010792601,0.000029622208,0.00011341629,0.00057146593,0.0068050753,0.0003219718,0.00022588027,0.00029708765,0.000010747223],"about_ca_topic_score_codex":0.009167374,"about_ca_topic_score_gemma":0.012695921,"teacher_disagreement_score":0.009167374,"about_ca_system_score_codex":0.00044539734,"about_ca_system_score_gemma":0.00026941544,"threshold_uncertainty_score":0.018228054},"labels":[],"label_agreement":null},{"id":"W4226188178","doi":"10.1099/mgen.0.000810","title":"Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Mycorrhizal Fungi and Plant Interactions","field":"Agricultural and Biological Sciences","cited_by":49,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Toronto; The Scarborough Hospital; University of Ottawa","funders":"","keywords":"Biology; Obligate; Genome; Phylogenetic tree; Genome size; Gene; Comparative genomics; Phylogenetics; Gene family; Genetics; Evolutionary biology; Most recent common ancestor; Genomics; Botany","score_opus":0.012402045482254754,"score_gpt":0.18740870348373612,"score_spread":0.17500665800148135,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4226188178","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99667335,0.0005045968,0.00094148057,0.00002640649,0.000003354069,0.0000058039673,0.0012402491,0.000055899978,0.0005488275],"genre_scores_gemma":[0.99201137,0.00029939433,0.0026962035,0.00002685365,0.000006536007,0.000014774686,0.004113143,0.000021737626,0.0008099459],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9999398,0.0000039180773,0.0000028196614,0.000024863251,0.000014794556,0.00001378803],"domain_scores_gemma":[0.99981445,0.000049492315,0.000058437123,0.000022543443,0.000015468799,0.000039682196],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000042522875,0.00027857066,0.0002163476,0.00042739528,0.00020958093,0.0002743003,0.0001822484,0.00019568104,0.0011349028],"category_scores_gemma":[0.00021244673,0.00009964922,0.00016147911,0.00041280265,0.00014360287,0.00019281234,0.00024717324,0.00029612475,0.00037695092],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00024886173,0.000022011885,0.016286662,0.00012824716,0.00002024796,0.00035235882,0.000110921465,0.00008750193,0.97360826,0.000117384574,0.000052407384,0.008965202],"study_design_scores_gemma":[0.000020161748,0.00030718007,0.83859456,0.00003135278,0.00010309675,0.0035052523,0.0003860421,0.0010580984,0.14736973,0.0003250599,0.008279674,0.000019754198],"about_ca_topic_score_codex":0.0010724437,"about_ca_topic_score_gemma":0.0024746952,"teacher_disagreement_score":0.0011349028,"about_ca_system_score_codex":0.00013652495,"about_ca_system_score_gemma":0.00018441897,"threshold_uncertainty_score":0.003796637},"labels":[],"label_agreement":null},{"id":"W4280525003","doi":"10.1099/mgen.0.000818","title":"Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":51,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McMaster University; Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Genome Canada; Cisco Systems; Simon Fraser University; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung; National Science Foundation","keywords":"Genome; Bacterial genome size; Phylogenetic tree; Computational biology; Biology; ENCODE; Visualization; Consistency (knowledge bases); Data mining; Genetics; Computer science; Gene; Artificial intelligence","score_opus":0.012586935830369128,"score_gpt":0.20645481252176467,"score_spread":0.19386787669139555,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4280525003","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.45358366,0.0015550625,0.43900436,0.0009649186,0.00026268495,0.00031509032,0.030359691,0.065769695,0.008184736],"genre_scores_gemma":[0.4770858,0.00063441764,0.4744165,0.00021704478,0.00006702499,0.0002889867,0.040776912,0.005059987,0.0014533693],"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9993262,0.00012376565,0.00005076088,0.00026587822,0.00015729778,0.00007612774],"domain_scores_gemma":[0.99853885,0.00069116807,0.00022199738,0.00016921009,0.00022883691,0.00015000881],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0019190958,0.0010480613,0.00092037104,0.0032293056,0.00076156424,0.0016287202,0.0010731387,0.00092924014,0.0051909713],"category_scores_gemma":[0.005567279,0.00057362264,0.001348644,0.002561241,0.0002731135,0.001761707,0.0023021377,0.0010816832,0.0019411129],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0033292996,0.00081841263,0.1446888,0.0025925348,0.0013201691,0.0015787132,0.0030291686,0.08872129,0.27393264,0.013417551,0.05281187,0.41375962],"study_design_scores_gemma":[0.0002176553,0.00040859944,0.090655945,0.0003215271,0.00044754407,0.00059658464,0.0011685016,0.77438325,0.069972716,0.021034699,0.04053488,0.0002580989],"about_ca_topic_score_codex":0.004418993,"about_ca_topic_score_gemma":0.004596156,"teacher_disagreement_score":0.0051909713,"about_ca_system_score_codex":0.000613189,"about_ca_system_score_gemma":0.0010431673,"threshold_uncertainty_score":0.017365515},"labels":[],"label_agreement":null},{"id":"W4280626237","doi":"10.1099/mgen.0.000833","title":"RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":117,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Wilfrid Laurier University","funders":"National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México; National Institutes of Health; Universidad Nacional Autónoma de México; Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","keywords":"Operon; Throughput; Biology; Computational biology; Transcriptional regulation; Variety (cybernetics); Regulation of gene expression; Gene; Genomics; Set (abstract data type); Resource (disambiguation); Transcription (linguistics); Transcription factor; Escherichia coli; Data science; Computer science; Genetics; Genome; Computer network; Artificial intelligence","score_opus":0.011685533921671595,"score_gpt":0.21357973087286822,"score_spread":0.20189419695119662,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4280626237","genre_codex":"dataset","genre_gemma":"dataset","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"dataset","genre_consensus":"dataset","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.016262736,0.0012330121,0.0056032697,0.00016535637,0.00007879489,0.00013811076,0.9675298,0.007304547,0.0016843596],"genre_scores_gemma":[0.007027149,0.00037747226,0.006712122,0.00008248688,0.000008741058,0.00037381318,0.98454607,0.00047464977,0.00039760533],"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","domain_scores_codex":[0.9970891,0.0005360001,0.00044492597,0.0008964656,0.00067826867,0.00035535064],"domain_scores_gemma":[0.99810874,0.00047331364,0.00027592687,0.0004989305,0.0004339772,0.00020912525],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0022275057,0.0024477225,0.0022152923,0.004110486,0.0013451363,0.0019933898,0.0025495926,0.0019169552,0.005357449],"category_scores_gemma":[0.004236034,0.0010969532,0.0022805994,0.0054716147,0.00064795755,0.0012752527,0.002762451,0.0021581755,0.0074587474],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0058595375,0.0010754139,0.064296566,0.022642601,0.0023923262,0.001022359,0.0010588756,0.035055704,0.1362188,0.00947308,0.6316396,0.08926506],"study_design_scores_gemma":[0.00089844933,0.00066166307,0.11265102,0.0013989131,0.0008770548,0.00068693695,0.00052455533,0.014401302,0.045644563,0.008594371,0.8130636,0.000597645],"about_ca_topic_score_codex":0.007498917,"about_ca_topic_score_gemma":0.008604818,"teacher_disagreement_score":0.007498917,"about_ca_system_score_codex":0.0012959137,"about_ca_system_score_gemma":0.0031534561,"threshold_uncertainty_score":0.017922461},"labels":[],"label_agreement":null},{"id":"W4295899950","doi":"10.1099/mgen.0.000864","title":"Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Chromium effects and bioremediation","field":"Environmental Science","cited_by":35,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Regina","funders":"","keywords":"Biology; Clade; Genus; Ecology; Phylogenetics; Genetics; Gene","score_opus":0.006173075031047325,"score_gpt":0.19027205205928654,"score_spread":0.1840989770282392,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4295899950","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99253285,0.0014406058,0.0015646205,0.00009281733,0.000009017359,0.000019943041,0.0032151605,0.000060460552,0.0010645696],"genre_scores_gemma":[0.9838616,0.0007913307,0.0041638287,0.000088830915,0.0000107260485,0.000034594075,0.010472418,0.000034799858,0.00054191344],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9997236,0.000021413773,0.00001863382,0.00011963365,0.000037366124,0.000079284364],"domain_scores_gemma":[0.9997125,0.00007582742,0.00006178864,0.000025305388,0.00006418877,0.000060400027],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00019867139,0.00043228478,0.0005314185,0.0019587995,0.00044246367,0.0007017092,0.00019224767,0.00036061704,0.0009360241],"category_scores_gemma":[0.00051087135,0.00013937693,0.0005718768,0.0016070787,0.00025749725,0.00041329284,0.00076651736,0.00042551348,0.00036005984],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0013667635,0.00014753109,0.23428258,0.00068554725,0.00027494255,0.000560078,0.0014612796,0.0012381746,0.70364463,0.0006420711,0.0007635334,0.054932814],"study_design_scores_gemma":[0.000028385046,0.00034450687,0.9641649,0.00011511841,0.00026947938,0.0013898683,0.0015138837,0.0050281705,0.015786096,0.0005790017,0.010734818,0.000045716457],"about_ca_topic_score_codex":0.0017866759,"about_ca_topic_score_gemma":0.0017269588,"teacher_disagreement_score":0.0019587995,"about_ca_system_score_codex":0.00029821164,"about_ca_system_score_gemma":0.00029046807,"threshold_uncertainty_score":0.0035524964},"labels":[],"label_agreement":null},{"id":"W4296553202","doi":"10.1099/mgen.0.000880","title":"Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antimicrobial Resistance in Staphylococcus","field":"Medicine","cited_by":26,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Agriculture and Agri-Food Canada; McMaster University; Public Health Agency of Canada; Dalhousie University; Simon Fraser University; University of Saskatchewan","funders":"Natural Sciences and Engineering Research Council of Canada; Research Nova Scotia; Simon Fraser University; Dalhousie University; Canadian Institutes of Health Research; Genome Canada; Canadian Institute for Advanced Research","keywords":"Enterococcus faecium; Mobile genetic elements; Biology; Resistome; Genetics; Antibiotic resistance; Genome; Context (archaeology); Horizontal gene transfer; Virulence; Evolutionary biology; Gene; Computational biology; Antibiotics","score_opus":0.08489041439927383,"score_gpt":0.30428848861846813,"score_spread":0.2193980742191943,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4296553202","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99629694,0.0006940016,0.0003693158,0.0001649164,0.000008093043,0.0000072408375,0.0016780872,0.00000668529,0.0007746971],"genre_scores_gemma":[0.99297875,0.00066168525,0.001423975,0.00028120776,0.000008453826,0.0000139768445,0.004193144,0.000017845894,0.00042103117],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9996743,0.00006153236,0.00002194008,0.00009809802,0.00005753405,0.00008663438],"domain_scores_gemma":[0.99947125,0.00011854894,0.00012312042,0.000046814563,0.00014477113,0.00009561198],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00038170486,0.00026902478,0.00048763977,0.0013927639,0.0007249321,0.0009676827,0.00018757443,0.0003815819,0.001013782],"category_scores_gemma":[0.0011187211,0.00013102955,0.0003993617,0.0019383406,0.00039927455,0.00027497587,0.0010348852,0.0003927091,0.00020383723],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0012939384,0.00015067968,0.73924625,0.0006016397,0.000747559,0.0019184407,0.008394429,0.0008585286,0.19532387,0.0008191836,0.001954819,0.048690744],"study_design_scores_gemma":[0.000008794302,0.00013655119,0.98499936,0.00008425321,0.00010873581,0.00069184415,0.0048173754,0.00034596067,0.0021033643,0.00019782037,0.006485347,0.000020556328],"about_ca_topic_score_codex":0.02291388,"about_ca_topic_score_gemma":0.03431002,"teacher_disagreement_score":0.02291388,"about_ca_system_score_codex":0.000563493,"about_ca_system_score_gemma":0.0008390469,"threshold_uncertainty_score":0.045561016},"labels":[],"label_agreement":null},{"id":"W4304004534","doi":"10.1099/mgen.0.000872","title":"A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Wheat and Barley Genetics and Pathology","field":"Agricultural and Biological Sciences","cited_by":23,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Alberta","funders":"","keywords":"Pyrenophora; Effector; Biology; Homology (biology); Pathogen; Fungal pathogen; Microbiology; Botany; Genetics; Gene; Cell biology","score_opus":0.01251104238095771,"score_gpt":0.19851655523758835,"score_spread":0.18600551285663064,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4304004534","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.93542874,0.0013597535,0.010123481,0.00009732225,0.00002183373,0.00013287224,0.051234733,0.00037333558,0.0012278557],"genre_scores_gemma":[0.65084654,0.0017594947,0.05074386,0.00010825124,0.00003219251,0.00021476857,0.29464442,0.00042359604,0.0012268081],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.999801,0.000019756495,0.00001667495,0.00009907835,0.000031722055,0.000031827567],"domain_scores_gemma":[0.99968123,0.000068719186,0.0000713541,0.000040504983,0.000057715246,0.00008052728],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003461165,0.00056366134,0.0005520665,0.0014934167,0.00043069053,0.0006230723,0.00029112876,0.00040904383,0.0011465859],"category_scores_gemma":[0.0006297706,0.00025540692,0.00064116035,0.0019148864,0.00015002111,0.0006807691,0.00076114334,0.00048543385,0.0004245603],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0011278981,0.0001679159,0.020199798,0.0011011988,0.000178691,0.0006516418,0.0008197647,0.001695242,0.93559706,0.00040168993,0.0012809698,0.036778133],"study_design_scores_gemma":[0.00022574478,0.0017911943,0.81134325,0.00026484017,0.00097618427,0.0035474105,0.0019619267,0.019210435,0.09341564,0.001101511,0.06602429,0.00013752299],"about_ca_topic_score_codex":0.0018253591,"about_ca_topic_score_gemma":0.0035981627,"teacher_disagreement_score":0.0018253591,"about_ca_system_score_codex":0.00030855066,"about_ca_system_score_gemma":0.0004890304,"threshold_uncertainty_score":0.0038357377},"labels":[],"label_agreement":null},{"id":"W4306176764","doi":"10.1099/mgen.0.000894","title":"Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli","year":2022,"lang":"en","type":"erratum","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université Laval","funders":"","keywords":"Escherichia coli; Principal (computer security); Antibiotic resistance; Biology; Microbiology; Antibiotics; Computational biology; Data science; Biotechnology; Computer science; Genetics; Gene; Computer security","score_opus":0.02773192507056364,"score_gpt":0.23832665001744846,"score_spread":0.21059472494688483,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4306176764","genre_codex":"editorial","genre_gemma":"other","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"other","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.00013109764,0.0010526973,0.00062229263,0.018341735,0.9768281,0.00002688981,0.00023355533,0.00020383846,0.0025597408],"genre_scores_gemma":[0.009421983,0.013846054,0.006988844,0.091687195,0.5074277,0.00027740974,0.0024118181,0.0013093922,0.36662966],"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","domain_scores_codex":[0.99728835,0.0004926848,0.0004432455,0.00041593678,0.0011209974,0.00023887769],"domain_scores_gemma":[0.9881126,0.0028393257,0.00046671412,0.00065404765,0.0069267205,0.0010005167],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0025300437,0.0033609697,0.0019900457,0.0031115573,0.0029770772,0.0041534165,0.0036108065,0.0061086486,0.041500542],"category_scores_gemma":[0.019651176,0.0015754168,0.0020256543,0.0019818358,0.0018635943,0.001980827,0.0012054925,0.006324158,0.038531225],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00002622157,0.000018897572,0.000050436312,0.00013509653,0.0000126056875,0.00022621045,0.000008863054,0.000058431706,0.00021824392,0.00028831558,0.99347174,0.0054848804],"study_design_scores_gemma":[0.0000516827,0.000093879906,0.0016830087,0.00024708788,0.00011315247,0.0009860082,0.00007617265,0.0006279984,0.0019941747,0.0014497247,0.99259806,0.00007912744],"about_ca_topic_score_codex":0.010209946,"about_ca_topic_score_gemma":0.020665662,"teacher_disagreement_score":0.041500542,"about_ca_system_score_codex":0.00308389,"about_ca_system_score_gemma":0.0025460615,"threshold_uncertainty_score":0.1388331},"labels":[],"label_agreement":null},{"id":"W4308732954","doi":"10.1099/mgen.0.000890","title":"Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Memorial University of Newfoundland","funders":"Natural Sciences and Engineering Research Council of Canada; Memorial University of Newfoundland","keywords":"Biology; Alphaproteobacteria; Horizontal gene transfer; Gene; Genetics; Prophage; Comparative genomics; Genome; Gammaproteobacteria; Rhodobacter; Genomics; Bacteriophage; Escherichia coli; 16S ribosomal RNA","score_opus":0.03845685026780113,"score_gpt":0.21846280008822858,"score_spread":0.18000594982042745,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4308732954","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9989489,0.00019414905,0.0004473292,0.000006032313,0.0000013181734,0.0000029696175,0.00012060048,0.000004276604,0.00027451303],"genre_scores_gemma":[0.9987664,0.000105884836,0.0005734844,0.000010454803,0.0000025740408,0.000006718274,0.00038568623,0.0000032769306,0.00014546799],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99986935,0.000017117492,0.000009798648,0.000043521544,0.000027761338,0.00003239432],"domain_scores_gemma":[0.9996587,0.00007405432,0.00009253745,0.000042895008,0.00005289951,0.00007887719],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00012737406,0.00014615383,0.00022884594,0.00075027894,0.0002131453,0.0003118639,0.00016122051,0.00022440289,0.0005211058],"category_scores_gemma":[0.00042130655,0.00011325262,0.00020956076,0.0006609871,0.00024645738,0.00022873162,0.00033615757,0.0002605839,0.0001383452],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00026553433,0.00002050209,0.020584214,0.000053981465,0.000030493477,0.00010364762,0.00018724217,0.000097677264,0.9744858,0.00013091158,0.000011571811,0.004028411],"study_design_scores_gemma":[0.000014533456,0.000417703,0.91337514,0.000026619362,0.00009700246,0.0015128641,0.0005183215,0.0015526743,0.080433495,0.00054752134,0.0014870263,0.000017148785],"about_ca_topic_score_codex":0.00058615475,"about_ca_topic_score_gemma":0.0006163028,"teacher_disagreement_score":0.00075027894,"about_ca_system_score_codex":0.0001359431,"about_ca_system_score_gemma":0.00016849909,"threshold_uncertainty_score":0.001743257},"labels":[],"label_agreement":null},{"id":"W4309830272","doi":"10.1099/mgen.0.000891","title":"Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance in Salmonella enterica subsp. enterica serovar Heidelberg","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Toronto; Public Health Ontario; University of Guelph; Agriculture and Agri-Food Canada; Canadian Food Inspection Agency; Western University; Public Health Agency of Canada","funders":"Ontario Veterinary College, University of Guelph; Genome Canada","keywords":"Salmonella enterica; Antibiotic resistance; Biology; Transmission (telecommunications); Salmonella; Antimicrobial; Serotype; Multiple drug resistance; Livestock; Microbiology; Plasmid; Biotechnology; Drug resistance; Antibiotics; Bacteria; Gene; Genetics; Ecology","score_opus":0.03345769763402606,"score_gpt":0.25529861733206427,"score_spread":0.2218409196980382,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4309830272","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9947425,0.00024880405,0.0031416963,0.00008672425,0.000005901507,0.00003074957,0.00042574108,0.00002523899,0.0012925579],"genre_scores_gemma":[0.9963834,0.00017370969,0.0027678316,0.00004598987,0.0000057234583,0.000009992604,0.00033175386,0.0000040494847,0.00027748302],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9992478,0.0002337952,0.00005109618,0.00020306185,0.00012417848,0.00014012556],"domain_scores_gemma":[0.9992513,0.00018027218,0.00029576977,0.000056984936,0.00013635354,0.000079221216],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008304655,0.00034428,0.00024804342,0.0015351269,0.00017884508,0.0007923043,0.00021309408,0.00036302538,0.0005587627],"category_scores_gemma":[0.0015088501,0.00019068239,0.0003182607,0.0011375427,0.00020915693,0.00032536636,0.00060212106,0.00023973486,0.0001351914],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00022670021,0.00013359518,0.9587968,0.000049376365,0.00013912436,0.00011876763,0.00029913615,0.00058654376,0.022447117,0.00021674177,0.0001676471,0.016818438],"study_design_scores_gemma":[0.0000069638195,0.00026948706,0.9923052,0.000023458153,0.00009552337,0.0003043286,0.0007300249,0.0025251443,0.0028791637,0.00018309214,0.0006678461,0.000009713647],"about_ca_topic_score_codex":0.009170689,"about_ca_topic_score_gemma":0.00972005,"teacher_disagreement_score":0.009170689,"about_ca_system_score_codex":0.00041642186,"about_ca_system_score_gemma":0.000501624,"threshold_uncertainty_score":0.01823461},"labels":[],"label_agreement":null},{"id":"W4311545199","doi":"10.1099/mgen.0.000905","title":"Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Fogarty International Center; National Institutes of Health; Génome Québec; Genome Canada","keywords":"Vibrio cholerae; Biology; Antibiotic resistance; Anaerobic exercise; Microbiology; Ciprofloxacin; Azithromycin; Cholera; Antibiotics; Genetics; Bacteria; Physiology","score_opus":0.010966724407922158,"score_gpt":0.24928420290244643,"score_spread":0.23831747849452428,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4311545199","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.998097,0.00075892435,0.00047591497,0.000083771054,0.000008545804,0.000003985019,0.00027949637,0.000013534566,0.0002787885],"genre_scores_gemma":[0.99913496,0.00026454532,0.0002648902,0.000028396884,0.000007397928,0.0000040318196,0.00019196041,0.0000071332347,0.000096660275],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9990274,0.00023815432,0.000080988604,0.0004152166,0.00009733788,0.00014094803],"domain_scores_gemma":[0.9983347,0.00058146706,0.00066892855,0.00018501327,0.00008925744,0.00014067553],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00092061795,0.00033840406,0.00045760788,0.0009037404,0.00036187665,0.0006779662,0.0004014816,0.0005987938,0.0016479525],"category_scores_gemma":[0.0018183076,0.0003570906,0.00065207033,0.0012419979,0.00059057726,0.00023456797,0.0005975614,0.0005887785,0.00014419413],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00043808925,0.00003721096,0.9819448,0.00004929275,0.0007366555,0.00033414701,0.00025631647,0.00031012078,0.0122145675,0.00011671428,0.0001207604,0.0034412183],"study_design_scores_gemma":[0.0000057104635,0.000033609886,0.99908817,0.0000059481554,0.00009587788,0.00012465706,0.00010913328,0.00017840044,0.00016345423,0.00006915822,0.0001207508,0.000005154017],"about_ca_topic_score_codex":0.006163121,"about_ca_topic_score_gemma":0.0056484314,"teacher_disagreement_score":0.006163121,"about_ca_system_score_codex":0.00020316198,"about_ca_system_score_gemma":0.00018651383,"threshold_uncertainty_score":0.012254477},"labels":[],"label_agreement":null},{"id":"W4311816724","doi":"10.1099/mgen.0.000883","title":"Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Shell (Canada); Vancouver Island University","funders":"School of Life Sciences, University of Technology Sydney; NSW Department of Primary Industries","keywords":"Gammaproteobacteria; Crassostrea; Outbreak; Biology; Pacific oyster; Vibrio; Diversity (politics); Ecology; Zoology; Fishery; Eastern oyster; Oyster; Virology; Bacteria","score_opus":0.01979882120816434,"score_gpt":0.22405376561559143,"score_spread":0.20425494440742709,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4311816724","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9987503,0.00009516508,0.00007881453,0.000012121391,0.0000025237152,0.000009209321,0.0008717025,0.0000028105094,0.0001773919],"genre_scores_gemma":[0.9947547,0.00026911392,0.00050532597,0.000054015924,0.000005506309,0.000032742355,0.0038333377,0.000006353397,0.00053902145],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9997532,0.000012997218,0.000023775356,0.00010094697,0.000050683087,0.00005847468],"domain_scores_gemma":[0.99968576,0.000034082008,0.000090869056,0.000015806947,0.000085483014,0.00008795966],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00017099046,0.00033869047,0.00039146908,0.00084697554,0.00040105032,0.0005377162,0.00015305178,0.00027054132,0.00033339064],"category_scores_gemma":[0.00036059174,0.00017631105,0.00042184364,0.0009250168,0.00030544735,0.00021024943,0.0005839273,0.00037330846,0.0001512153],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0004368672,0.00011978281,0.40391484,0.00014873983,0.00009459005,0.0003815613,0.0017939642,0.0002863734,0.5863281,0.000037169422,0.0001681625,0.006289937],"study_design_scores_gemma":[0.0000028771178,0.00012642857,0.99498194,0.000010892999,0.00003097896,0.00017750278,0.0007848205,0.00021220649,0.0032626933,0.000013144027,0.00039007454,0.0000063300004],"about_ca_topic_score_codex":0.0068174815,"about_ca_topic_score_gemma":0.009124797,"teacher_disagreement_score":0.0068174815,"about_ca_system_score_codex":0.00020629872,"about_ca_system_score_gemma":0.00030410287,"threshold_uncertainty_score":0.013555586},"labels":[],"label_agreement":null},{"id":"W4311816931","doi":"10.1099/mgen.0.000906","title":"Large-scale comparative genomics to refine the organization of the global Salmonella enterica population structure","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":8,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University; University of British Columbia","funders":"Canadian Institutes of Health Research; Genome British Columbia; Michael Smith Health Research BC; Genome Canada","keywords":"Serotype; In silico; Polyphyly; Biology; Salmonella enterica; Salmonella; Population; Typing; Genetics; Multiple Loci VNTR Analysis; Genomics; Multilocus sequence typing; Computational biology; Genome; Phylogenetics; Microbiology; Gene; Tandem repeat; Medicine","score_opus":0.014470606297591417,"score_gpt":0.2220600092011294,"score_spread":0.20758940290353797,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4311816931","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.86880565,0.0027725743,0.11599166,0.00040579564,0.000057052963,0.00010008476,0.006952091,0.00063660624,0.004278499],"genre_scores_gemma":[0.8978912,0.0012578254,0.0882131,0.00024065688,0.00003735977,0.00008154468,0.011476647,0.00018283328,0.00061875244],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.99974924,0.00006747051,0.000012329998,0.000106450236,0.000029276132,0.00003522207],"domain_scores_gemma":[0.9997003,0.00013612476,0.000058365236,0.00004330194,0.000030958632,0.000030959167],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00080731895,0.0004996417,0.00046403607,0.0013989074,0.0003246466,0.00061689806,0.00030260737,0.00036364226,0.0010953033],"category_scores_gemma":[0.0008983921,0.00018729315,0.00062076683,0.0014520282,0.00023167625,0.00048294803,0.0006336047,0.0007296865,0.0002991468],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00048374728,0.00023021456,0.026868762,0.00074376597,0.00050239457,0.0004906104,0.0010454463,0.014033553,0.8853668,0.0060284245,0.0011003388,0.06310593],"study_design_scores_gemma":[0.0001721328,0.0015101682,0.62208754,0.00030372743,0.0012527639,0.0019211228,0.0018462363,0.17004648,0.113939136,0.020234067,0.06648225,0.00020437417],"about_ca_topic_score_codex":0.0018791434,"about_ca_topic_score_gemma":0.0042209355,"teacher_disagreement_score":0.0018791434,"about_ca_system_score_codex":0.0004885044,"about_ca_system_score_gemma":0.00042715762,"threshold_uncertainty_score":0.0042695403},"labels":[],"label_agreement":null},{"id":"W4312207459","doi":"10.1099/mgen.0.000909","title":"At the threshold of symbiosis: the genome of obligately endosymbiotic ‘Candidatus Nebulobacter yamunensis’ is almost indistinguishable from that of a cultivable strain","year":2022,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Protist diversity and phylogeny","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of British Columbia","funders":"Gordon and Betty Moore Foundation","keywords":"Obligate; Biology; Endosymbiosis; Candidatus; Genome; Symbiosis; Buchnera; Strain (injury); Genetics; Evolutionary biology; Gene; Botany; Bacteria; Plastid","score_opus":0.014735666304368502,"score_gpt":0.19958118323492058,"score_spread":0.18484551693055207,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4312207459","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9974516,0.0008660642,0.00072160456,0.00003480559,0.000009409621,0.000005096784,0.00046275384,0.000037297672,0.00041131183],"genre_scores_gemma":[0.9962436,0.00022569383,0.0010775529,0.000060074948,0.0000046915698,0.000011642617,0.0019096669,0.000023113425,0.0004439782],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9997907,0.000016718728,0.000014739993,0.00009568998,0.000045290715,0.000036822035],"domain_scores_gemma":[0.999701,0.00006891048,0.00008570103,0.000057228473,0.000036408943,0.00005074951],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00012760784,0.00028075223,0.0002744366,0.0002405729,0.00023055705,0.0006420451,0.00021580554,0.0005110267,0.0006475973],"category_scores_gemma":[0.0003612259,0.00016941463,0.00030731413,0.00036712273,0.00033241155,0.00045092468,0.0004574727,0.00047224452,0.00026834797],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00013852569,0.000007593018,0.0026141272,0.00007191679,0.000019467047,0.0000775073,0.000090264955,0.000037359856,0.9950087,0.00004562868,0.000018890833,0.0018700525],"study_design_scores_gemma":[0.000022122353,0.00043247323,0.54347736,0.000046123827,0.00019330112,0.0031303945,0.000633189,0.0009985572,0.4444069,0.00037937408,0.0062321206,0.00004811682],"about_ca_topic_score_codex":0.0011139377,"about_ca_topic_score_gemma":0.0011870294,"teacher_disagreement_score":0.0011139377,"about_ca_system_score_codex":0.00014181227,"about_ca_system_score_gemma":0.00017099454,"threshold_uncertainty_score":0.0022149086},"labels":[],"label_agreement":null},{"id":"W4317815831","doi":"10.1099/mgen.0.000908","title":"The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Research Data Management Practices","field":"Computer Science","cited_by":19,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"St. John’s Health Sciences Centre; McMaster University; University of Alberta; Saskatchewan Disease Control Laboratory; Public Health Agency of Canada; Simon Fraser University; Institut National de Santé Publique du Québec; Nova Scotia Health Authority; BC Centre for Disease Control; Hospital for Sick Children; Public Health Ontario; University of British Columbia","funders":"Canadian Institutes of Health Research; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University; Genome British Columbia; Michael Smith Health Research BC; Genome Canada","keywords":"Metadata; Data sharing; Computer science; Data science; Harmonization; Interoperability; Big data; Data integration; Usability; World Wide Web; Database; Data mining; Medicine","score_opus":0.07868323319902724,"score_gpt":0.31252340920585275,"score_spread":0.2338401760068255,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4317815831","genre_codex":"methods","genre_gemma":"software","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"software","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.0035680968,0.0004456913,0.49052337,0.0009879002,0.0003428288,0.0009031328,0.031251416,0.46633947,0.005638081],"genre_scores_gemma":[0.046845365,0.0008689334,0.79156315,0.0018562196,0.0001536894,0.00229903,0.07915699,0.070321046,0.0069355615],"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9877033,0.0024951336,0.0018805029,0.0026365905,0.004717736,0.0005666803],"domain_scores_gemma":[0.97406363,0.013672065,0.0015594263,0.0072503425,0.0022709912,0.0011834003],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.020990163,0.003785553,0.0027868743,0.007479324,0.0017285526,0.007727626,0.004681956,0.0020457834,0.025169186],"category_scores_gemma":[0.04017836,0.0029469193,0.003175255,0.006022203,0.0020152337,0.010330472,0.013193928,0.0060785855,0.013774905],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0024177057,0.00056232855,0.010890552,0.0035211407,0.0010400078,0.0017912448,0.004738895,0.010869834,0.019519797,0.036129806,0.42438716,0.48413157],"study_design_scores_gemma":[0.0010846305,0.0003677248,0.011437729,0.0020776025,0.00034729595,0.0012642253,0.0013156567,0.10907005,0.057596836,0.089782275,0.72473156,0.0009244566],"about_ca_topic_score_codex":0.0047317836,"about_ca_topic_score_gemma":0.0042047626,"teacher_disagreement_score":0.025169186,"about_ca_system_score_codex":0.0017239748,"about_ca_system_score_gemma":0.005147915,"threshold_uncertainty_score":0.11100793},"labels":[],"label_agreement":null},{"id":"W4319294603","doi":"10.1099/mgen.0.000887","title":"The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":8,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"","funders":"Medical Research Council; Directorate for Biological Sciences; Imperial College London; Department of Health and Social Care; National Institute for Health Research Health Protection Research Unit; UK Dementia Research Institute; National Institute for Health and Care Research; NIHR Imperial Biomedical Research Centre; Biotechnology and Biological Sciences Research Council; Huo Family Foundation; MRC-PHE Centre for Environment and Health; UK Research and Innovation; British Heart Foundation; Wellcome Trust","keywords":"Lineage (genetic); Clade; Phylogenetic tree; Quarter (Canadian coin); Transmission (telecommunications); Biology; Demography; Alpha (finance); Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Competition (biology); Coronavirus disease 2019 (COVID-19); Evolutionary biology; Genetics; Medicine; Internal medicine; Disease; Gene; Geography; Ecology; Infectious disease (medical specialty)","score_opus":0.1882129535716628,"score_gpt":0.3845554961234446,"score_spread":0.1963425425517818,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4319294603","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9984719,0.0001916858,0.0003201203,0.000014208715,0.0000020416253,0.00004260804,0.00046141222,0.0000043763735,0.00049156253],"genre_scores_gemma":[0.9973604,0.00016091812,0.00071821234,0.000041793213,0.0000068028157,0.00006628359,0.0008139941,0.0000041380135,0.0008274591],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99932265,0.00021425413,0.000071112176,0.00014797565,0.00012628174,0.00011770495],"domain_scores_gemma":[0.9981053,0.00031337372,0.0006602897,0.00009610434,0.000652171,0.00017286018],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008170779,0.00029184017,0.0004373071,0.0010799319,0.0005828292,0.0008168828,0.00030291072,0.0004641606,0.0009983068],"category_scores_gemma":[0.0019505306,0.00040467025,0.00018004533,0.0006499757,0.00033156996,0.000502393,0.00074087374,0.00025155226,0.00034895557],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00069609523,0.00006622923,0.95935863,0.00009417382,0.000042775042,0.00069871196,0.0037581162,0.0002382142,0.028604066,0.000062567655,0.00020758082,0.0061728605],"study_design_scores_gemma":[0.0000068231184,0.00024060856,0.99668026,0.000013823241,0.000009732239,0.0004755305,0.001125535,0.00018478771,0.0007123573,0.000018454282,0.0005250613,0.000007109727],"about_ca_topic_score_codex":0.040375456,"about_ca_topic_score_gemma":0.09210201,"teacher_disagreement_score":0.040375456,"about_ca_system_score_codex":0.0006873354,"about_ca_system_score_gemma":0.0003154763,"threshold_uncertainty_score":0.0802809},"labels":[],"label_agreement":null},{"id":"W4323035821","doi":"10.1099/mgen.0.000929","title":"Epidemiological cluster identification using multiple data sources: an approach using logistic regression","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Data-Driven Disease Surveillance","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University","funders":"European Commission","keywords":"Cluster analysis; Pairwise comparison; Spatial epidemiology; Cluster (spacecraft); Data mining; Computational biology; Epidemiology; Logistic regression; Biology; Computer science; Statistics; Mathematics; Medicine","score_opus":0.2749071077727216,"score_gpt":0.38850209636470295,"score_spread":0.11359498859198136,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4323035821","genre_codex":"methods","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":"methods","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.02247619,0.0007944709,0.97244734,0.0014627307,0.00011343888,0.00041598387,0.0005453652,0.00111473,0.0006297916],"genre_scores_gemma":[0.29132724,0.00072282634,0.7021579,0.00036386828,0.0003285599,0.0010358789,0.0017596182,0.000400333,0.0019037616],"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.95165247,0.034195423,0.0022769442,0.007116095,0.0037614915,0.0009974781],"domain_scores_gemma":[0.91007024,0.07059736,0.0063983877,0.0060907668,0.0058730533,0.0009702832],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.055075504,0.002880214,0.0046947883,0.0138802035,0.0026257632,0.0060129906,0.009475983,0.0037729107,0.002875927],"category_scores_gemma":[0.093096405,0.002254408,0.006492586,0.014097838,0.0017172195,0.0054491484,0.006882819,0.0061117383,0.0016623283],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0013227442,0.00131599,0.20343153,0.0012579571,0.00794606,0.0017408342,0.002991494,0.31956232,0.0015121262,0.026987486,0.009280547,0.422651],"study_design_scores_gemma":[0.000052032196,0.00008421651,0.003995524,0.00009702666,0.00021841183,0.00015912135,0.00038462505,0.9756821,0.0003362998,0.016617093,0.0022927576,0.00008086095],"about_ca_topic_score_codex":0.015594813,"about_ca_topic_score_gemma":0.009798156,"teacher_disagreement_score":0.055075504,"about_ca_system_score_codex":0.0023228065,"about_ca_system_score_gemma":0.003838594,"threshold_uncertainty_score":0.2912706},"labels":[],"label_agreement":null},{"id":"W4323036397","doi":"10.1099/mgen.0.000949","title":"From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":63,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Dalhousie Medical Research Foundation","keywords":"Metagenomics; Taxonomic rank; Database; Computer science; Biological classification; Reference database; Range (aeronautics); Precision and recall; Data mining; Information retrieval; Biology; Taxon; Ecology; Gene; Evolutionary biology; Engineering","score_opus":0.044888458707746534,"score_gpt":0.28636265601695066,"score_spread":0.2414741973092041,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4323036397","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.61558276,0.026907608,0.17449635,0.0056652455,0.002758537,0.0012950184,0.027902335,0.12935169,0.016040487],"genre_scores_gemma":[0.5905423,0.0041664666,0.3186477,0.0063532935,0.0002796133,0.0017688824,0.05244755,0.023072567,0.0027216244],"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.97147757,0.008842502,0.0052112676,0.0074739074,0.0055954293,0.0013992724],"domain_scores_gemma":[0.9185194,0.051814012,0.0022200476,0.01791797,0.0075551835,0.0019733165],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.042218592,0.0033969062,0.0034223022,0.0035903496,0.0022278703,0.008914732,0.007838952,0.0044721295,0.005345659],"category_scores_gemma":[0.12581739,0.0023353102,0.0023237648,0.005414647,0.0012157926,0.014330718,0.0057505188,0.006181227,0.0077047814],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.015601762,0.0033281217,0.12862556,0.008006623,0.0037144206,0.0019809562,0.0034475357,0.030153777,0.091798976,0.009647227,0.1300642,0.5736309],"study_design_scores_gemma":[0.0037402401,0.002879248,0.064734526,0.0036939618,0.0025256327,0.006981132,0.0041511166,0.26291937,0.30972454,0.059520904,0.27571538,0.0034139396],"about_ca_topic_score_codex":0.0035486324,"about_ca_topic_score_gemma":0.0035818508,"teacher_disagreement_score":0.042218592,"about_ca_system_score_codex":0.001389489,"about_ca_system_score_gemma":0.0017791104,"threshold_uncertainty_score":0.22327596},"labels":[],"label_agreement":null},{"id":"W4353020380","doi":"10.1099/mgen.0.000958","title":"Rapid adaptations of Legionella pneumophila to the human host","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Legionella and Acanthamoeba research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Fonds de recherche du Québec – Nature et technologies; Japan Society for the Promotion of Science; Carl Tryggers Stiftelse för Vetenskaplig Forskning; Science for Life Laboratory; Folkhälsomyndigheten; Vetenskapsrådet; Public Health Agency","keywords":"Legionella pneumophila; Biology; Gene; Population; Microbiology; Legionnaires' disease; Host (biology); Virology; Genetics; Bacteria","score_opus":0.02828146836205718,"score_gpt":0.27372277210682416,"score_spread":0.24544130374476697,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4353020380","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99851245,0.00045735607,0.0003332465,0.000054598608,0.0000067946244,0.000007082298,0.000077798264,0.00001531363,0.000535392],"genre_scores_gemma":[0.9990414,0.00020620067,0.00030928684,0.000049385144,0.000009229559,0.0000053853305,0.00013607458,0.000006693746,0.0002363593],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9995203,0.000108792585,0.000024842608,0.00014693395,0.000096771546,0.000102399026],"domain_scores_gemma":[0.99963164,0.00005638021,0.00012077997,0.00006552917,0.000053974538,0.0000716689],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00027242306,0.0002995509,0.00039044415,0.00031974574,0.00025984136,0.00049973914,0.00019051394,0.00039285232,0.001410349],"category_scores_gemma":[0.0007008337,0.00013476075,0.00026003344,0.00020849986,0.00033156932,0.0003053396,0.00047977694,0.00033977733,0.00029575205],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0007667921,0.00012869568,0.124410965,0.00010252629,0.00008058424,0.0017831969,0.0004460408,0.00033260678,0.86096877,0.0002934222,0.00024236806,0.010444048],"study_design_scores_gemma":[0.00004772645,0.0024603955,0.8170281,0.0000528639,0.00015182976,0.015800392,0.0011735233,0.001095367,0.15218449,0.00051057676,0.0094227055,0.000072006944],"about_ca_topic_score_codex":0.0005846304,"about_ca_topic_score_gemma":0.0005334034,"teacher_disagreement_score":0.001410349,"about_ca_system_score_codex":0.00027965638,"about_ca_system_score_gemma":0.00021749901,"threshold_uncertainty_score":0.0047180653},"labels":[],"label_agreement":null},{"id":"W4365135538","doi":"10.1099/mgen.0.000979","title":"Comparing genomic variant identification protocols for Candida auris","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antifungal resistance and susceptibility","field":"Medicine","cited_by":15,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Commissariat Général à l'Investissement; Centers for Disease Control and Prevention; Agence Nationale de la Recherche; National Institute of Allergy and Infectious Diseases; Division of Intramural Research, National Institute of Allergy and Infectious Diseases; Broad Institute; Wellcome Trust; Medical Research Council; Canadian Institute for Advanced Research; National Institutes of Health; U.S. Department of Health and Human Services","keywords":"Biology; Single-nucleotide polymorphism; Phylogenetic tree; Clade; Computational biology; Genetics; Concordance; Genome-wide association study; SNP; Population; Gene; Medicine; Genotype","score_opus":0.0570976395604316,"score_gpt":0.3247589607406333,"score_spread":0.2676613211802017,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4365135538","genre_codex":"empirical","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.737038,0.0036160506,0.24131404,0.00070429017,0.000416397,0.0023095387,0.0066348566,0.0038447587,0.004122046],"genre_scores_gemma":[0.4420395,0.0018032747,0.5316289,0.0006899607,0.00006342262,0.0024355021,0.018338915,0.0014600036,0.0015404131],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.98822916,0.0027152775,0.0025188548,0.0028904062,0.0030054494,0.0006409158],"domain_scores_gemma":[0.98847735,0.0053105433,0.0009725228,0.002173744,0.0027568256,0.000309041],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.011874138,0.00078418496,0.00073601597,0.00214318,0.00092351803,0.0018638809,0.0014277841,0.0011952382,0.0011497473],"category_scores_gemma":[0.031304844,0.00097514,0.0019461587,0.0018380501,0.00083316525,0.001026476,0.0019300182,0.0016794653,0.00091537734],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0030177583,0.0004805277,0.048379637,0.0018114945,0.0010247431,0.0003815683,0.00207261,0.017200548,0.7460475,0.0033894964,0.0035137977,0.17268036],"study_design_scores_gemma":[0.00017799214,0.0019354317,0.09648588,0.00024218498,0.0009345878,0.0014632259,0.0007681107,0.042987138,0.82876265,0.003570373,0.022307256,0.0003650534],"about_ca_topic_score_codex":0.0044143256,"about_ca_topic_score_gemma":0.00617814,"teacher_disagreement_score":0.011874138,"about_ca_system_score_codex":0.0013339376,"about_ca_system_score_gemma":0.0014824605,"threshold_uncertainty_score":0.06279719},"labels":[],"label_agreement":null},{"id":"W4365443776","doi":"10.1099/mgen.0.000981","title":"Single nucleotide variants in Pseudomonas aeruginosa populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Cystic Fibrosis Research Advances","field":"Medicine","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McGill Genome Centre; Université Laval; University of Calgary; McGill University Health Centre; McGill University","funders":"Fonds de Recherche du Québec - Santé; Genome Canada; Canadian Institutes of Health Research; Deutsche Akademie der Naturforscher Leopoldina - Nationale Akademie der Wissenschaften; Génome Québec; Cystic Fibrosis Canada","keywords":"Cystic fibrosis; Sputum; Microbiome; Internal medicine; Biology; Lung; Receiver operating characteristic; Pseudomonas aeruginosa; Single-nucleotide polymorphism; Medicine; Immunology; Genotype; Bioinformatics; Pathology; Genetics; Gene","score_opus":0.013926648695835512,"score_gpt":0.26094864137711654,"score_spread":0.24702199268128103,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4365443776","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.998004,0.00017718939,0.0014589984,0.000056557994,0.000004853778,0.0000049704654,0.0001304243,0.000016680162,0.00014620417],"genre_scores_gemma":[0.9990225,0.00004548619,0.0005974399,0.000022227727,0.000006027984,0.0000036666675,0.00020794703,0.000003809823,0.000090898444],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9995716,0.00012996883,0.000034848483,0.00014634266,0.000061952436,0.00005535377],"domain_scores_gemma":[0.9981306,0.0010803608,0.0003614544,0.00016351418,0.00014158478,0.00012239313],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0010646315,0.0004313082,0.00031142417,0.00047593843,0.00032198432,0.0006849053,0.00019872103,0.00056561065,0.0005987224],"category_scores_gemma":[0.0034489168,0.00022597346,0.00046356767,0.0002760663,0.0003248407,0.00033054955,0.00044959845,0.00088021613,0.00026375082],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00020317125,0.00006202664,0.9789443,0.000011885163,0.000118094234,0.00007647873,0.000080054764,0.0056946427,0.0040186895,0.000029932258,0.00015211615,0.010608735],"study_design_scores_gemma":[0.000014425054,0.00029121563,0.9023059,0.000023901106,0.00011281629,0.00040566505,0.00020018833,0.09229529,0.0034093426,0.00053507794,0.0003821053,0.000024115045],"about_ca_topic_score_codex":0.004229095,"about_ca_topic_score_gemma":0.0057520894,"teacher_disagreement_score":0.004229095,"about_ca_system_score_codex":0.00023836052,"about_ca_system_score_gemma":0.00023506276,"threshold_uncertainty_score":0.008408964},"labels":[],"label_agreement":null},{"id":"W4367319211","doi":"10.1099/mgen.0.000988","title":"Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":39,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McMaster University","funders":"National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Institutes of Health","keywords":"Horizontal gene transfer; Biology; Metagenomics; Microbiome; Gene; Evolutionary biology; Computational biology; Genetics; Genome; Bacterial genome size; Phylum; Identification (biology); Clade; Phylogenetics; Ecology","score_opus":0.02881578258156842,"score_gpt":0.22904649861821322,"score_spread":0.2002307160366448,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4367319211","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.91258496,0.0013483348,0.040206116,0.00034251562,0.000103995466,0.00029643867,0.0341094,0.005856908,0.005151219],"genre_scores_gemma":[0.71270806,0.00072145613,0.22030067,0.00032941013,0.000052523275,0.0006080002,0.061850354,0.0017822917,0.0016472242],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99878305,0.0002470979,0.00010003777,0.000398344,0.0003101534,0.00016128234],"domain_scores_gemma":[0.99840075,0.0005290451,0.00030483218,0.00019459048,0.00035857118,0.00021222871],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002197479,0.0013396408,0.0010729776,0.0052529774,0.0013936483,0.0021881608,0.0009815595,0.0008997627,0.0026071924],"category_scores_gemma":[0.004988339,0.0005718815,0.0016741108,0.0054844664,0.0006076597,0.0008810297,0.0023740353,0.0012845999,0.0015176241],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0027191073,0.0008122657,0.3242539,0.002292164,0.0017135651,0.0015150713,0.0062276763,0.028811427,0.47508338,0.006313113,0.014371785,0.13588655],"study_design_scores_gemma":[0.0002499341,0.0014241353,0.42891917,0.000576217,0.0009981093,0.0028884155,0.0043710396,0.36824527,0.1040211,0.0108136255,0.07696307,0.00052989525],"about_ca_topic_score_codex":0.0043977406,"about_ca_topic_score_gemma":0.005256874,"teacher_disagreement_score":0.0052529774,"about_ca_system_score_codex":0.00082279596,"about_ca_system_score_gemma":0.0012725428,"threshold_uncertainty_score":0.011621475},"labels":[],"label_agreement":null},{"id":"W4376641528","doi":"10.1099/mgen.0.001025","title":"Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":7,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Queen's University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; Gammaproteobacteria; Replicon; Genome; Genetics; Horizontal gene transfer; Gene; Evolutionary biology; Genome evolution","score_opus":0.008469510793395418,"score_gpt":0.22723532567688,"score_spread":0.2187658148834846,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4376641528","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9932288,0.0028013778,0.0020033629,0.00003361682,0.0000073892916,0.000023110804,0.0005119341,0.000029623483,0.0013608406],"genre_scores_gemma":[0.9954163,0.0011200845,0.0020048828,0.000041753774,0.000009676058,0.000019453582,0.00076937367,0.000015220137,0.0006033394],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9997048,0.000037772217,0.000020699637,0.000111668356,0.00006315885,0.00006184032],"domain_scores_gemma":[0.99920624,0.00014749911,0.0002277819,0.00014137058,0.0001668234,0.00011026228],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00021807794,0.00036428258,0.00029555388,0.0016671338,0.000384433,0.00071257097,0.00026150627,0.00036218308,0.0006213525],"category_scores_gemma":[0.0007952861,0.00023947489,0.00040482037,0.001038,0.00034525403,0.00047170534,0.00079875166,0.00036191026,0.00035985254],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0005571489,0.00007248582,0.24364443,0.0003606811,0.00015679396,0.00046385173,0.0006501129,0.0006968471,0.6965565,0.0006712988,0.00013230942,0.056037497],"study_design_scores_gemma":[0.000013795176,0.00024755904,0.95880425,0.000077617005,0.00013814864,0.001383271,0.00039339915,0.0016791939,0.032130193,0.0007386456,0.0043531945,0.00004077961],"about_ca_topic_score_codex":0.0011010634,"about_ca_topic_score_gemma":0.0008802959,"teacher_disagreement_score":0.0016671338,"about_ca_system_score_codex":0.00020190985,"about_ca_system_score_gemma":0.00029346207,"threshold_uncertainty_score":0.0021893382},"labels":[],"label_agreement":null},{"id":"W4377011370","doi":"10.1099/mgen.0.001002","title":"A global survey of Salmonella plasmids and their associations with antimicrobial resistance","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":19,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Public Health Agency of Canada","funders":"Government of Canada; Public Health Agency; Public Health Agency of Canada","keywords":"Plasmid; Biology; Salmonella; Genetics; Serotype; Salmonella enterica; Horizontal gene transfer; Replicon; Gene; Genome; Microbiology; Bacteria","score_opus":0.01142618487166453,"score_gpt":0.22854232721614254,"score_spread":0.217116142344478,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4377011370","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99417454,0.00024805995,0.0019830274,0.000019160992,0.000002247432,0.000015726371,0.0029009897,0.000052394953,0.00060387026],"genre_scores_gemma":[0.98296976,0.00037792602,0.0036129237,0.000025511721,0.0000071694158,0.000032727316,0.012498528,0.00002541563,0.00045010837],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99958795,0.00007215962,0.000024382492,0.00015439512,0.00008610455,0.000074870375],"domain_scores_gemma":[0.999326,0.00012258482,0.00020903992,0.00007797705,0.00016109875,0.00010334892],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005327696,0.00044464396,0.00033211283,0.0019068242,0.00019142273,0.00045863696,0.0001796809,0.00024440448,0.00072234235],"category_scores_gemma":[0.00093366735,0.00014143145,0.00037815145,0.0018538102,0.00024473653,0.00040031486,0.0007832611,0.0002627326,0.00037172638],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0002942933,0.000080611455,0.80154586,0.0002266767,0.00018858694,0.00016562306,0.00056273665,0.0016924312,0.15993087,0.00021449922,0.00060596265,0.03449187],"study_design_scores_gemma":[0.0000060895236,0.000304006,0.98825073,0.000013723503,0.00006607264,0.0003210968,0.0003921215,0.0013994663,0.0068441783,0.000088506655,0.0023017933,0.0000123212885],"about_ca_topic_score_codex":0.0011682187,"about_ca_topic_score_gemma":0.0014351043,"teacher_disagreement_score":0.0019068242,"about_ca_system_score_codex":0.00021819213,"about_ca_system_score_gemma":0.00031743132,"threshold_uncertainty_score":0.0028176308},"labels":[],"label_agreement":null},{"id":"W4377564504","doi":"10.1099/mgen.0.001015","title":"Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Institute of Genetics; Lotte Foundation; Ministry of Education, Culture, Sports, Science and Technology; Japan Society for the Promotion of Science; Meiji University; Sumitomo Foundation","keywords":"Lactic acid; Operon; Bacteria; Escherichia coli; Biochemistry; Biology; Lactate dehydrogenase; Gene; Chemistry; Genetics; Enzyme","score_opus":0.00962300492091871,"score_gpt":0.20058496789134433,"score_spread":0.1909619629704256,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4377564504","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9632544,0.006669185,0.02535136,0.0006848514,0.00006724168,0.00004400642,0.0013254071,0.0005404709,0.0020630695],"genre_scores_gemma":[0.9788327,0.0013406854,0.015755512,0.00034458554,0.000022100201,0.000027714284,0.0014473451,0.00009096511,0.002138392],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9996375,0.0000699185,0.000028021392,0.00013073337,0.00007211401,0.00006177374],"domain_scores_gemma":[0.99977297,0.00005439736,0.000045300447,0.000037271202,0.00004247689,0.000047649184],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00029602484,0.0005476132,0.00054072804,0.00035341486,0.00016711933,0.0006000046,0.00027400054,0.00040927398,0.0011234425],"category_scores_gemma":[0.00030221153,0.00021718134,0.0004947909,0.0003326471,0.00037814802,0.00039669714,0.0005116099,0.00064334675,0.0006083959],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00014199228,0.000018100025,0.00045280764,0.00006414667,0.0000030421177,0.00006166419,0.000031451043,0.00014799922,0.99511826,0.00009951627,0.000033628006,0.0038273386],"study_design_scores_gemma":[0.0000321811,0.00018772333,0.018386614,0.0000398611,0.000036412344,0.0005900331,0.00014207204,0.003433707,0.97109884,0.00030007947,0.0057176244,0.00003482219],"about_ca_topic_score_codex":0.0012387258,"about_ca_topic_score_gemma":0.0010978878,"teacher_disagreement_score":0.0012387258,"about_ca_system_score_codex":0.00052505656,"about_ca_system_score_gemma":0.00035070546,"threshold_uncertainty_score":0.0038095713},"labels":[],"label_agreement":null},{"id":"W4384119784","doi":"10.1099/mgen.0.001061","title":"The gut microbiome and resistome of conventionally vs. pasture-raised pigs","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Agriculture and Agri-Food Canada","funders":"Agriculture and Agri-Food Canada","keywords":"Resistome; Biology; Microbiome; Metagenomics; Context (archaeology); Antimicrobial; Antibiotic resistance; Pasture; Microbiology; Biotechnology; Antibiotics; Ecology; Bioinformatics; Genetics; Gene; Integron","score_opus":0.008068754214436653,"score_gpt":0.23663319062760044,"score_spread":0.2285644364131638,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4384119784","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.999328,0.00007825866,0.00014882417,0.000009040542,0.0000031422385,0.0000054043094,0.000263907,0.0000021927513,0.00016115626],"genre_scores_gemma":[0.9970407,0.00016634379,0.00085431087,0.00009855486,0.0000074953027,0.0000252843,0.0011408053,0.0000057153716,0.00066076935],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99981755,0.000023920535,0.000012080468,0.00008126861,0.000026362046,0.000038909115],"domain_scores_gemma":[0.99989295,0.000017742292,0.00003743859,0.000010995395,0.000016162696,0.000024669245],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00017100268,0.00027136126,0.00027450465,0.00037038868,0.00020744669,0.000331514,0.00011852196,0.00035806865,0.0007160242],"category_scores_gemma":[0.00019422037,0.00017409405,0.0003348955,0.0003187523,0.0002412857,0.0002871704,0.0003449686,0.00031350975,0.00012664341],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0007087963,0.00010446368,0.10513229,0.00009618626,0.00011364964,0.00031319418,0.00029163843,0.00012150297,0.88641894,0.000043269785,0.00006490239,0.006591113],"study_design_scores_gemma":[0.000007989881,0.00058627623,0.9877472,0.000010997817,0.00006357062,0.0003594768,0.00037670438,0.00029672778,0.010069702,0.000026077143,0.00044651295,0.000008829884],"about_ca_topic_score_codex":0.00097265694,"about_ca_topic_score_gemma":0.0015419847,"teacher_disagreement_score":0.00097265694,"about_ca_system_score_codex":0.000120696815,"about_ca_system_score_gemma":0.000118743694,"threshold_uncertainty_score":0.0023953319},"labels":[],"label_agreement":null},{"id":"W4387563735","doi":"10.1099/mgen.0.001112","title":"Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial infections and disease research","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal","funders":"International Development Research Centre; Compute Canada; Université de Sherbrooke","keywords":"Biology; Pathogen; Genomics; Mycoplasma; Microbiology; Genetics; Computational biology; Genome; Gene","score_opus":0.026164277126114376,"score_gpt":0.27705927926581003,"score_spread":0.2508950021396957,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4387563735","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99680567,0.0007841428,0.0004316695,0.000020797084,0.000004821153,0.000009843522,0.0012992044,0.0000146251405,0.0006291751],"genre_scores_gemma":[0.99023086,0.0006620729,0.002065596,0.00005798576,0.000015040197,0.000032396423,0.0056215054,0.000023278766,0.0012912524],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99990666,0.0000087340695,0.00000528603,0.000041155297,0.000017324193,0.000020886506],"domain_scores_gemma":[0.99987376,0.000022734695,0.00003697416,0.0000074464433,0.000024144798,0.00003489527],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009272409,0.00034417544,0.00031269868,0.00088095164,0.00027576744,0.00038595006,0.00018170703,0.00025217424,0.00069836277],"category_scores_gemma":[0.00017198134,0.00010186084,0.00029000707,0.00066443783,0.00013078838,0.00022435113,0.00025343,0.00023430621,0.00023190213],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00024844136,0.000034189576,0.006079689,0.00011806766,0.000021667463,0.00015505055,0.0002642917,0.00008424583,0.9888755,0.00004878277,0.000051900624,0.0040180767],"study_design_scores_gemma":[0.000009042781,0.00052276294,0.9462401,0.00003684864,0.00011177004,0.001135508,0.00052271335,0.0011578443,0.04615242,0.000076776756,0.0040157633,0.000018418847],"about_ca_topic_score_codex":0.0016939064,"about_ca_topic_score_gemma":0.0014637586,"teacher_disagreement_score":0.0016939064,"about_ca_system_score_codex":0.00022362328,"about_ca_system_score_gemma":0.0001420739,"threshold_uncertainty_score":0.0033680797},"labels":[],"label_agreement":null},{"id":"W4388023526","doi":"10.1099/mgen.0.001125","title":"Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Mansoura University; Animal and Plant Health Agency; Trent University; Nottingham Trent University","keywords":"Microbiology; Biology; Pseudomonas aeruginosa; Fosfomycin; Antibiotic resistance; Ciprofloxacin; Multilocus sequence typing; Virulence; Antimicrobial; Genotype; Antibiotics; Gene; Bacteria; Genetics","score_opus":0.007035721026428798,"score_gpt":0.21456383960139172,"score_spread":0.20752811857496292,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4388023526","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9989987,0.00018888974,0.00010859374,0.000032402495,0.000002699702,0.00001825269,0.00047747538,0.0000028534423,0.0001701538],"genre_scores_gemma":[0.9967866,0.00046142482,0.0007204003,0.000073757445,0.000013855825,0.000020773057,0.0013387942,0.0000045681645,0.00057983695],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9995975,0.000035172456,0.0000625569,0.00009817396,0.00012577904,0.000080749385],"domain_scores_gemma":[0.9994134,0.00007115629,0.0001988649,0.000029557053,0.00020196923,0.00008519168],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00018045197,0.00030822286,0.00034754223,0.001118395,0.00047101048,0.00070593954,0.000206269,0.0004026186,0.00047765917],"category_scores_gemma":[0.0007538961,0.00016007134,0.00030716328,0.0017615092,0.0002725114,0.00034000055,0.00044612525,0.00028787187,0.00018870854],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00056804676,0.00034651687,0.5533194,0.0004144071,0.000107867236,0.0079617975,0.0045216414,0.0005115432,0.40464023,0.00007304915,0.0003829959,0.027152602],"study_design_scores_gemma":[0.0000062060667,0.00037757398,0.97504187,0.00001985555,0.000060434413,0.0044651073,0.0032596688,0.0002230918,0.015025102,0.000019338506,0.0014815595,0.000020240215],"about_ca_topic_score_codex":0.0057583787,"about_ca_topic_score_gemma":0.0060137142,"teacher_disagreement_score":0.0057583787,"about_ca_system_score_codex":0.00028092277,"about_ca_system_score_gemma":0.0004624409,"threshold_uncertainty_score":0.011449695},"labels":[],"label_agreement":null},{"id":"W4388946150","doi":"10.1099/mgen.0.001143","title":"Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Amoebic Infections and Treatments","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Dalhousie University; University of Alberta","funders":"Canadian Institutes of Health Research; European Commission; Univerzita Komenského v Bratislave; Univerzita Karlova v Praze; Grantová Agentura České Republiky; H2020 European Research Council; Ministerstvo Školství, Mládeže a Tělovýchovy","keywords":"Organelle; Biology; Catabolism; Mitochondrion; Metabolism; Extremophile; Biochemistry; Citric acid cycle; Metabolic pathway; Metabolic network; Cell biology; Enzyme; Thermophile","score_opus":0.019748403887139637,"score_gpt":0.2850693573685533,"score_spread":0.2653209534814137,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4388946150","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99825007,0.00045769595,0.0005397458,0.000008981936,0.0000026536272,0.0000042360866,0.0002768612,0.000012301944,0.00044741508],"genre_scores_gemma":[0.9956291,0.0004393746,0.0016754996,0.00001599514,0.0000053888875,0.000010978327,0.0017634241,0.0000116909605,0.00044859416],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9999287,0.000006743421,0.0000068941654,0.000029363911,0.000014204675,0.000014016763],"domain_scores_gemma":[0.9998385,0.000027167784,0.000047443536,0.000011113107,0.000027970418,0.000047786467],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009442325,0.00027938,0.00021905135,0.0007935404,0.00037328372,0.00036084815,0.00018534146,0.00030609657,0.00057273626],"category_scores_gemma":[0.0002609178,0.00015959905,0.00032114156,0.0003728518,0.00016899161,0.00037682249,0.00037685176,0.0001582297,0.00028043173],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00053506676,0.000038293812,0.04285042,0.0002633333,0.0000855037,0.0004625713,0.00043128702,0.0006167523,0.94787526,0.00025118524,0.000047000874,0.006543279],"study_design_scores_gemma":[0.000021698554,0.0005669352,0.93112886,0.000058036505,0.0001891718,0.002200852,0.00082180597,0.007116053,0.051925886,0.00047078682,0.0054657874,0.00003403331],"about_ca_topic_score_codex":0.0006583623,"about_ca_topic_score_gemma":0.00074153347,"teacher_disagreement_score":0.0007935404,"about_ca_system_score_codex":0.00015844891,"about_ca_system_score_gemma":0.00016478254,"threshold_uncertainty_score":0.0019159913},"labels":[],"label_agreement":null},{"id":"W4389083107","doi":"10.1099/mgen.0.001141","title":"Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993–2019","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Pneumonia and Respiratory Infections","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Public Health Agency of Canada; Women and Children’s Health Research Institute; University of Alberta","funders":"Ministry of Economic Development and Trade, Government of Alberta; Pfizer Canada; Merck Canada; Government of Alberta; Pfizer","keywords":"Biology; Multilocus sequence typing; Antibiotic resistance; Microbiology; Streptococcus pneumoniae; Typing; Serotype; Carriage; Tigecycline; Tetracycline; Molecular epidemiology; Virology; Genotype; Antibiotics; Medicine; Genetics; Gene","score_opus":0.008675246165884103,"score_gpt":0.22831491935321752,"score_spread":0.2196396731873334,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4389083107","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9667413,0.0025277447,0.0004635019,0.00028316662,0.00003531479,0.00010668893,0.02518445,0.00004863166,0.0046091992],"genre_scores_gemma":[0.95128006,0.003105863,0.0018135636,0.00051437126,0.00002808518,0.000061211475,0.03765474,0.00003107928,0.00551096],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99925786,0.000021556369,0.000031257372,0.00011128617,0.000364318,0.00021384079],"domain_scores_gemma":[0.99873084,0.000044951623,0.00015347957,0.000025823443,0.00079437305,0.00025056416],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00043594898,0.0005241855,0.00032813317,0.002970565,0.00148815,0.001245692,0.00053772464,0.00033783237,0.00085780624],"category_scores_gemma":[0.0010360893,0.0002646584,0.00041712387,0.005783914,0.0005510316,0.00013658055,0.000693538,0.00036703015,0.00026809124],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0009715706,0.000074803545,0.9181045,0.00035719867,0.00013746569,0.0022154558,0.0043542734,0.0013960922,0.031857323,0.00036118046,0.0062188827,0.03395124],"study_design_scores_gemma":[0.000008322356,0.000041764924,0.98902434,0.00006408253,0.00003486187,0.00031733545,0.001650631,0.00026689447,0.00081280345,0.000020295596,0.0077483836,0.000010305297],"about_ca_topic_score_codex":0.97651064,"about_ca_topic_score_gemma":0.9852761,"teacher_disagreement_score":0.023489356,"about_ca_system_score_codex":0.01212925,"about_ca_system_score_gemma":0.018795248,"threshold_uncertainty_score":0.08800423},"labels":[],"label_agreement":null},{"id":"W4389180569","doi":"10.1099/mgen.0.001149","title":"Plasmid-encoded lactose metabolism and mobilized colistin resistance (mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Saskatchewan Research Council (Canada); National Research Council Canada; University of Regina","funders":"H2020 Marie Skłodowska-Curie Actions; Natural Sciences and Engineering Research Council of Canada; Saskatchewan Health Research Foundation","keywords":"Salmonella enterica; Plasmid; Microbiology; Salmonella; Serotype; Colistin; Lactose; Gene; Biology; Bacteria; Genetics; Antibiotics; Food science","score_opus":0.012340628534870349,"score_gpt":0.22908613835164376,"score_spread":0.21674550981677343,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4389180569","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9994616,0.000122058285,0.00013238023,0.0000088518955,0.0000018469945,0.0000034694947,0.00017805722,0.000003856044,0.000087833156],"genre_scores_gemma":[0.9975535,0.00020205649,0.00073925615,0.000015754138,0.0000028307966,0.00000762178,0.001114921,0.0000053838526,0.000358658],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9997837,0.000015795822,0.000030934945,0.00006786287,0.00004975102,0.000051938867],"domain_scores_gemma":[0.99982977,0.00002028462,0.0000730625,0.000017649285,0.000030360354,0.000028778288],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00014882613,0.00035451475,0.00028391936,0.00097144424,0.0001926633,0.00038007653,0.00020956015,0.0002757246,0.00024135105],"category_scores_gemma":[0.00033664762,0.00032663284,0.00039688984,0.0007190908,0.00023612432,0.00017706394,0.0004506063,0.00020166204,0.00012727195],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0002805859,0.000059277158,0.103475966,0.00009541412,0.00007336188,0.0005247279,0.0006998107,0.00027109322,0.8886531,0.000059875314,0.000049376198,0.0057573346],"study_design_scores_gemma":[0.000011203807,0.00025840098,0.9195481,0.00001106819,0.00011342357,0.0010981916,0.00068550825,0.00042266582,0.07685582,0.000035686604,0.0009436194,0.000016210257],"about_ca_topic_score_codex":0.0050177895,"about_ca_topic_score_gemma":0.004558082,"teacher_disagreement_score":0.0050177895,"about_ca_system_score_codex":0.00035890285,"about_ca_system_score_gemma":0.00026122667,"threshold_uncertainty_score":0.009977162},"labels":[],"label_agreement":null},{"id":"W4389627602","doi":"10.1099/mgen.0.001145","title":"Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications","year":2023,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University; McMaster University; Western University; Public Health Agency of Canada; Dalhousie University","funders":"Institute of Genetics; U.S. National Library of Medicine; National Institutes of Health; Simon Fraser University; European Molecular Biology Laboratory","keywords":"Metadata; Object (grammar); Data science; Computer science; Public health interventions; Public health; Data model (GIS); Relevance (law); World Wide Web; Artificial intelligence; Medicine; Political science","score_opus":0.14298818131963031,"score_gpt":0.3272449415921956,"score_spread":0.18425676027256527,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4389627602","genre_codex":"methods","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.0077963457,0.00020863656,0.9751761,0.003739563,0.00047132955,0.00056351774,0.0017857889,0.00589044,0.0043682954],"genre_scores_gemma":[0.033213723,0.00024736335,0.9559518,0.0015814987,0.00016971,0.0004792255,0.004383142,0.0011395317,0.002834014],"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"not_applicable","domain_scores_codex":[0.9823514,0.007006869,0.003334574,0.0020726277,0.0040407865,0.001193637],"domain_scores_gemma":[0.9566304,0.0070263566,0.0023070371,0.0237715,0.008176864,0.002087916],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.02844291,0.0009317669,0.0012487699,0.0028775518,0.002895174,0.014947023,0.0048787384,0.0039728885,0.0020332285],"category_scores_gemma":[0.03416576,0.001422684,0.003091098,0.0034074087,0.004088,0.013453687,0.010257046,0.0051190862,0.003678196],"study_design_candidate":"not_applicable","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00083810685,0.00062188745,0.034050964,0.0006919383,0.00016386059,0.0010810025,0.005142838,0.04098416,0.012021991,0.6935424,0.057838,0.1530228],"study_design_scores_gemma":[0.00015225793,0.00030283193,0.0023972378,0.00066661,0.00011532546,0.0007968852,0.001509379,0.15923205,0.01579681,0.27391273,0.5447866,0.00033140188],"about_ca_topic_score_codex":0.011019722,"about_ca_topic_score_gemma":0.014701705,"teacher_disagreement_score":0.02844291,"about_ca_system_score_codex":0.0033811454,"about_ca_system_score_gemma":0.013274768,"threshold_uncertainty_score":0.15042228},"labels":[],"label_agreement":null},{"id":"W4390578629","doi":"10.1099/mgen.0.001169","title":"Complete genomes of Clostridium botulinum type B(F) isolates associated with a 1995 foodborne botulism outbreak from commercial pâté reveals a recombination event disrupting the ntnh gene","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Botulinum Toxin and Related Neurological Disorders","field":"Medicine","cited_by":2,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Health Canada","funders":"Health Canada","keywords":"Botulism; Clostridium botulinum; Biology; Plasmid; Microbiology; Gene; Genome; Food poisoning; Outbreak; Genetics; Virology; Toxin","score_opus":0.02267160704440953,"score_gpt":0.2510214404074146,"score_spread":0.22834983336300504,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4390578629","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9790341,0.0007881721,0.0010099856,0.00014822865,0.000016510801,0.00009759129,0.017876789,0.000031426684,0.0009971472],"genre_scores_gemma":[0.90036577,0.0010167545,0.006747065,0.00024700892,0.000013545825,0.00010521342,0.088305585,0.000061833496,0.0031372278],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99982613,0.000014033689,0.00001350164,0.000041802585,0.00005251847,0.00005206153],"domain_scores_gemma":[0.99968624,0.00006271406,0.000064667365,0.000022070035,0.000101061574,0.000063273605],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00016759551,0.00034008402,0.0002946311,0.0006494855,0.0004862693,0.00039973692,0.00027665994,0.0004772059,0.0007891629],"category_scores_gemma":[0.0006715514,0.00018266647,0.00028822423,0.0012716207,0.00017838232,0.00015371066,0.00023442821,0.00046795968,0.00034125178],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0014457484,0.00019797073,0.02767168,0.00040523103,0.000104829385,0.0020440123,0.0014991455,0.00077550084,0.9453691,0.00024534852,0.0013014775,0.018939935],"study_design_scores_gemma":[0.00010664564,0.0008382164,0.898636,0.00008226974,0.0002489592,0.0046633263,0.0018334128,0.0018262329,0.06216277,0.00019461321,0.029345943,0.00006158917],"about_ca_topic_score_codex":0.04123377,"about_ca_topic_score_gemma":0.057215508,"teacher_disagreement_score":0.04123377,"about_ca_system_score_codex":0.00084452087,"about_ca_system_score_gemma":0.0007932996,"threshold_uncertainty_score":0.08198756},"labels":[],"label_agreement":null},{"id":"W4390590447","doi":"10.1099/mgen.0.001167","title":"Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial Natural Products and Biosynthesis","field":"Medicine","cited_by":3,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Health Sciences Centre; McMaster University Medical Centre","funders":"National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Center for Complementary and Integrative Health; National Cancer Institute; National Institutes of Health","keywords":"Computational biology; Biology; Gene cluster; Metric (unit); Diversity (politics); Natural product; Evolutionary biology; Gene; Genetics; Engineering","score_opus":0.01781790905919284,"score_gpt":0.22658484185811123,"score_spread":0.2087669327989184,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4390590447","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.93960863,0.01975941,0.010673709,0.004146079,0.00012691146,0.00008703103,0.017583765,0.00038181484,0.0076326746],"genre_scores_gemma":[0.92496365,0.011555678,0.031137738,0.0016121883,0.00012479049,0.00012259117,0.029056141,0.00015805867,0.0012690945],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9993098,0.00012754089,0.00005035215,0.00024098766,0.00015554213,0.000115687915],"domain_scores_gemma":[0.998779,0.00035084164,0.00016615093,0.00020252167,0.0002632541,0.00023832681],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0013053729,0.00044424445,0.0008051973,0.0019636333,0.000593853,0.0015897441,0.0004386987,0.00037985574,0.0021315902],"category_scores_gemma":[0.0015584389,0.00018113117,0.000581385,0.002762916,0.0003858112,0.0011311107,0.0010959134,0.0010886473,0.0007084379],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.001205655,0.00027622972,0.18720238,0.0017560683,0.0004100891,0.0006518039,0.001873368,0.002419604,0.5906864,0.003057749,0.00552091,0.20493986],"study_design_scores_gemma":[0.000057283884,0.0006247306,0.8138019,0.0006116367,0.00024137342,0.0020616162,0.0040084887,0.0037650075,0.030229447,0.01105564,0.13340278,0.0001401284],"about_ca_topic_score_codex":0.0023536326,"about_ca_topic_score_gemma":0.0061314343,"teacher_disagreement_score":0.0023536326,"about_ca_system_score_codex":0.00046688635,"about_ca_system_score_gemma":0.0008616881,"threshold_uncertainty_score":0.0071308613},"labels":[],"label_agreement":null},{"id":"W4390590654","doi":"10.1099/mgen.0.001165","title":"An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McGill University; Institut National de la Recherche Scientifique","funders":"Fonds de Recherche du Québec - Santé; Huck Institutes of the Life Sciences; Canadian Institutes of Health Research; Alliance de recherche numérique du Canada; U.S. Department of Agriculture; Canada Research Chairs; Department for International Development; Bill and Melinda Gates Foundation","keywords":"Mycobacterium tuberculosis complex; Reference genome; Biology; Genome; Genetics; Sequence (biology); Comparative genomics; Whole genome sequencing; Computational biology; Evolutionary biology; Genomics; Mycobacterium tuberculosis; Tuberculosis; Gene","score_opus":0.034311258216834735,"score_gpt":0.26199993800201504,"score_spread":0.22768867978518031,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4390590654","genre_codex":"methods","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":"methods","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.39183423,0.0010963547,0.58452886,0.00058070745,0.00041743764,0.0003069056,0.009817272,0.007718249,0.003700019],"genre_scores_gemma":[0.3108131,0.00034559253,0.6495986,0.00033598146,0.00005628372,0.00029311058,0.03479228,0.002174108,0.0015909489],"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.99787617,0.00049028307,0.0002117845,0.00077158946,0.0004901283,0.00016008026],"domain_scores_gemma":[0.9968521,0.00086026866,0.00032832852,0.0007454671,0.0010475975,0.00016619735],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0030568314,0.00074854743,0.001030245,0.0013169629,0.0011480941,0.0015471367,0.0013197636,0.0013073212,0.0024318614],"category_scores_gemma":[0.008731329,0.00064193807,0.001177846,0.0018845872,0.0005176234,0.0013001721,0.001401056,0.0023467063,0.0015709334],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0018705786,0.00052953896,0.016985912,0.0009720115,0.0001949788,0.0008642231,0.0012466171,0.033433784,0.8346553,0.016445514,0.0048466558,0.08795486],"study_design_scores_gemma":[0.00024639303,0.0013660106,0.03549395,0.00027462366,0.00041637215,0.0012948345,0.0004658655,0.25057438,0.5988831,0.016208334,0.094425045,0.0003511909],"about_ca_topic_score_codex":0.0027551898,"about_ca_topic_score_gemma":0.0047948076,"teacher_disagreement_score":0.0030568314,"about_ca_system_score_codex":0.0011329676,"about_ca_system_score_gemma":0.001541832,"threshold_uncertainty_score":0.01616621},"labels":[],"label_agreement":null},{"id":"W4390794905","doi":"10.1099/mgen.0.001174","title":"Genomic and clinical characteristics of campylobacteriosis in Australia","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Agriculture and Agri-Food Canada","funders":"National Health and Medical Research Council; Agrifutures Australia; Department of Health, State Government of Victoria; University of Melbourne; Meat and Livestock Australia; Queensland Health; ACT Health; Australian Government; Medical Research Council; NSW Ministry of Health; Department of Health and Aged Care, Australian Government; Massey University; Hunter New England Local Health District; U.S. Department of Health and Human Services","keywords":"Campylobacteriosis; Virulence; Odds ratio; Campylobacter jejuni; Disease; Campylobacter; Multilocus sequence typing; Medicine; Odds; Internal medicine; Biology; Genotype; Gene; Genetics; Logistic regression; Bacteria","score_opus":0.043015828280245576,"score_gpt":0.28765580158907783,"score_spread":0.24463997330883225,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4390794905","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99942505,0.00006983547,0.000036138612,0.000021485263,9.927969e-7,0.000013210946,0.00013582005,0.0000012111622,0.0002962715],"genre_scores_gemma":[0.999401,0.00007038821,0.00011937979,0.000022928549,0.0000021752276,0.000010869327,0.00019991188,9.2912796e-7,0.00017251965],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9996007,0.000066417524,0.000057106066,0.000102960745,0.0001047051,0.000068166315],"domain_scores_gemma":[0.9989743,0.00008667591,0.00041095188,0.00004496541,0.00025962817,0.00022349588],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00033204097,0.00019616749,0.00024422348,0.0010549156,0.0005396656,0.00043698226,0.00022730458,0.00032857768,0.0009707956],"category_scores_gemma":[0.0016927957,0.0002826408,0.00017072361,0.0009175797,0.00051884993,0.00031420964,0.00065631716,0.00026078845,0.00013620208],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.000050352523,0.00003409138,0.99329984,0.000028218954,0.000015257663,0.00029379092,0.000894225,0.00004329162,0.0027960648,0.000016326552,0.00009876293,0.002429766],"study_design_scores_gemma":[9.969227e-7,0.0000368266,0.9992988,0.0000041596204,0.0000026714754,0.00025429725,0.00021808814,0.000048585203,0.000036086563,0.0000091054135,0.000088750036,0.0000015543989],"about_ca_topic_score_codex":0.029412765,"about_ca_topic_score_gemma":0.02890983,"teacher_disagreement_score":0.029412765,"about_ca_system_score_codex":0.0005801166,"about_ca_system_score_gemma":0.00038070604,"threshold_uncertainty_score":0.058483124},"labels":[],"label_agreement":null},{"id":"W4390908590","doi":"10.1099/mgen.0.001179","title":"Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antifungal resistance and susceptibility","field":"Medicine","cited_by":13,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of British Columbia; McMaster University","funders":"Medical Research Council; Alliance de recherche numérique du Canada; University of British Columbia; Simon Fraser University; Sidra Medicine; McMaster University; Hamad Medical Corporation","keywords":"Candida glabrata; Biology; Population; Genetic diversity; Genetics; Transmission (telecommunications); Microbiology; Candida albicans; Medicine","score_opus":0.023843914838308035,"score_gpt":0.28473970527368747,"score_spread":0.2608957904353794,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4390908590","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9989281,0.00016723822,0.0004826892,0.000027546308,0.0000023069983,0.000007799898,0.0002055759,0.000006565906,0.0001722173],"genre_scores_gemma":[0.9989956,0.0000851957,0.0003619554,0.000049874252,0.0000050097756,0.0000056347535,0.00038589764,0.000002017774,0.00010879719],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9996742,0.00005575178,0.00002283684,0.00013039102,0.000047142825,0.00006961911],"domain_scores_gemma":[0.9996537,0.00006949523,0.0001385908,0.000031792213,0.0000685717,0.00003790821],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003996876,0.00023599807,0.00022890618,0.00090371707,0.0003041197,0.00045440794,0.00018314851,0.0003162837,0.0009770488],"category_scores_gemma":[0.0007482305,0.00010154314,0.00025927663,0.00086209056,0.00026104169,0.00014067878,0.00027878294,0.0003378599,0.00017220106],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00029011353,0.000099239405,0.8292539,0.000065802255,0.00025831707,0.0005117303,0.0022210497,0.0010025334,0.14920641,0.00031132982,0.00038153311,0.016397936],"study_design_scores_gemma":[0.0000070361198,0.000103836624,0.9965162,0.000009084841,0.000031485502,0.00029587498,0.00043744524,0.00079007586,0.0012967905,0.00009258499,0.0004137876,0.0000057497496],"about_ca_topic_score_codex":0.0053997478,"about_ca_topic_score_gemma":0.004279318,"teacher_disagreement_score":0.0053997478,"about_ca_system_score_codex":0.0003277386,"about_ca_system_score_gemma":0.00016208924,"threshold_uncertainty_score":0.010736585},"labels":[],"label_agreement":null},{"id":"W4391230939","doi":"10.1099/mgen.0.001186","title":"Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Animal Disease Management and Epidemiology","field":"Agricultural and Biological Sciences","cited_by":6,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal; University of Saskatchewan","funders":"National Key Research and Development Program of China; Higher Education Discipline Innovation Project; Priority Academic Program Development of Jiangsu Higher Education Institutions","keywords":"African swine fever virus; Biology; Codon usage bias; Clade; Phylogenetic tree; Genome; Adaptation (eye); Gene; Coding region; Genetics; Virus; Host (biology); Host adaptation; Evolutionary biology; Phylogenetics; Virology; Zoology","score_opus":0.03756748206318438,"score_gpt":0.2345583487589889,"score_spread":0.1969908666958045,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4391230939","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99856466,0.0003868557,0.00051451835,0.000012658485,0.0000039778997,0.0000056338968,0.00030526915,0.000005337684,0.00020113986],"genre_scores_gemma":[0.9974197,0.00018142951,0.0013958298,0.00001771288,0.0000048246384,0.0000076032984,0.0008375075,0.0000053979616,0.00013000841],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99982846,0.000047529556,0.000019262152,0.00004840888,0.000031239957,0.000025060557],"domain_scores_gemma":[0.99961793,0.000106077234,0.00014352261,0.000028186692,0.000050761555,0.000053516294],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00026130863,0.00016213422,0.00019652338,0.0010396081,0.00024513915,0.00023800852,0.00007449298,0.00016154935,0.00039599853],"category_scores_gemma":[0.00054590066,0.000077120654,0.00027427732,0.0009974693,0.00014818396,0.00012931872,0.00013479777,0.00021055335,0.00013489395],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00073950464,0.0001098422,0.34484076,0.0002264435,0.00022917501,0.0007677507,0.0007212836,0.0006072363,0.61822504,0.0003107086,0.00028694948,0.032935284],"study_design_scores_gemma":[0.000012892074,0.00037640287,0.96959287,0.00004026052,0.00017010812,0.0018519637,0.00041356584,0.0032523826,0.021002676,0.00019720997,0.0030683773,0.000021232685],"about_ca_topic_score_codex":0.0006152288,"about_ca_topic_score_gemma":0.0016442719,"teacher_disagreement_score":0.0010396081,"about_ca_system_score_codex":0.00012452161,"about_ca_system_score_gemma":0.00016895939,"threshold_uncertainty_score":0.0013819337},"labels":[],"label_agreement":null},{"id":"W4391983336","doi":"10.1099/mgen.0.001180","title":"Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Institute of Genetics; Japan Agency for Medical Research and Development","keywords":"Resistome; Microbiome; Antimicrobial; Metagenomics; Antibiotics; Biology; Antibiotic resistance; Microbiology; Bioinformatics; Genetics; Gene; Integron","score_opus":0.025818073256010526,"score_gpt":0.25011763044938096,"score_spread":0.22429955719337044,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4391983336","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9991487,0.00021946695,0.00022699183,0.00003227,0.0000032986602,0.000009058604,0.00023420561,0.0000029809155,0.00012294602],"genre_scores_gemma":[0.99756867,0.00019702264,0.0011357686,0.00017940861,0.000010747653,0.00003992099,0.0005130145,0.000004589003,0.0003508306],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9992093,0.00027759196,0.00006290704,0.00018075058,0.00015795232,0.00011145952],"domain_scores_gemma":[0.99894005,0.00026317453,0.00039982673,0.00008179729,0.00020795446,0.000107198204],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008160652,0.00028260605,0.00032846743,0.0004056484,0.00039663963,0.00040783273,0.00020580598,0.00035205242,0.00086578797],"category_scores_gemma":[0.001719319,0.00016942674,0.00040707705,0.000389374,0.00026738056,0.00025751392,0.0005185244,0.00026315878,0.00014189396],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0012235908,0.00038742254,0.8709501,0.00025215666,0.00050442567,0.0002159836,0.0013515438,0.00018974049,0.09779181,0.00003318584,0.0003072713,0.026792767],"study_design_scores_gemma":[0.0000060549132,0.0006565662,0.9954769,0.000016507614,0.0000778795,0.000082162514,0.00043607876,0.00018158455,0.0027009964,0.000019322395,0.00033797967,0.000007886198],"about_ca_topic_score_codex":0.004470786,"about_ca_topic_score_gemma":0.010980928,"teacher_disagreement_score":0.004470786,"about_ca_system_score_codex":0.0002344772,"about_ca_system_score_gemma":0.00031398234,"threshold_uncertainty_score":0.008889556},"labels":[],"label_agreement":null},{"id":"W4392166113","doi":"10.1099/mgen.0.001156","title":"Exploring the genetic basis of natural resistance to microcins","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada; International Development Research Centre","keywords":"Salmonella enterica; Bacteriocin; Biology; Klebsiella pneumoniae; Escherichia coli; Microbiology; Enterobacteriaceae; Gene; Antimicrobial; Antibiotic resistance; Genetics; Antibiotics","score_opus":0.021385044416663775,"score_gpt":0.22059090165310438,"score_spread":0.1992058572364406,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4392166113","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9988049,0.00016561923,0.0004558725,0.000017443243,0.0000017717875,0.00001494697,0.00031938014,0.000005279637,0.00021484416],"genre_scores_gemma":[0.9979728,0.00020904452,0.0008885451,0.000024862904,0.000003519204,0.000013838673,0.00061298214,0.000007404723,0.00026691295],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.99974614,0.00004315238,0.000021364402,0.00007891267,0.00004941494,0.00006105184],"domain_scores_gemma":[0.9996475,0.00009756378,0.00012710028,0.000032337295,0.000047575373,0.000047866542],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00014406878,0.00032184317,0.0003297853,0.0008446214,0.0001644802,0.00023744366,0.00020635713,0.00028112158,0.00080391084],"category_scores_gemma":[0.00045090428,0.00015508068,0.00030739442,0.00057636807,0.00025602255,0.00011201268,0.00031545767,0.00029874608,0.00015089137],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0004575285,0.000096866504,0.06982901,0.000060144746,0.00007330768,0.00045225467,0.00017745238,0.00012446567,0.92487115,0.00007351049,0.000039209295,0.003745149],"study_design_scores_gemma":[0.000014711222,0.0005944932,0.9193105,0.000021035788,0.00011931925,0.002568148,0.00045253403,0.00093337655,0.07468917,0.00008001806,0.0011984757,0.000018184706],"about_ca_topic_score_codex":0.0014406533,"about_ca_topic_score_gemma":0.0013054544,"teacher_disagreement_score":0.0014406533,"about_ca_system_score_codex":0.00017251662,"about_ca_system_score_gemma":0.00014929874,"threshold_uncertainty_score":0.0028645396},"labels":[],"label_agreement":null},{"id":"W4392950477","doi":"10.1099/mgen.0.001215","title":"Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada; University of Alberta; Universities Space Research Association","keywords":"Biology; Conserved sequence; Genetics; Evolutionary biology; Enterobacteriaceae; Molecular evolution; Sequence (biology); Phylogenetics; Gene; Computational biology; Peptide sequence; Escherichia coli","score_opus":0.011565455155522996,"score_gpt":0.21912318153702715,"score_spread":0.20755772638150416,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4392950477","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99583423,0.0008722322,0.0022478853,0.000050375438,0.000002752973,0.000006155001,0.00020938383,0.000024380537,0.0007526006],"genre_scores_gemma":[0.9967906,0.0003545812,0.0021971825,0.000045465404,0.0000041284457,0.0000050889494,0.0003359839,0.000013457325,0.00025340964],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9998388,0.000030080151,0.000015289668,0.000051208972,0.000029804765,0.000034841647],"domain_scores_gemma":[0.9996315,0.00008741844,0.00012027237,0.00004028343,0.00006211008,0.00005842247],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00024177876,0.00018240626,0.00024994594,0.0012386598,0.00027225012,0.00042126534,0.00016316431,0.00034619236,0.00070891296],"category_scores_gemma":[0.0005557047,0.00014957717,0.0002274698,0.0009393333,0.00027010473,0.00044289854,0.0003476804,0.00039278096,0.0002661237],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00028565337,0.000045749413,0.12960538,0.00015221849,0.000080718826,0.00039949612,0.00058159523,0.0013168501,0.8467818,0.00058576535,0.000102646794,0.020062067],"study_design_scores_gemma":[0.000010577948,0.00019578176,0.95450014,0.000045880905,0.000077971876,0.0017152841,0.0007128386,0.005619361,0.031326607,0.0012037833,0.00455495,0.00003675008],"about_ca_topic_score_codex":0.00061441574,"about_ca_topic_score_gemma":0.0012092682,"teacher_disagreement_score":0.0012386598,"about_ca_system_score_codex":0.00022924645,"about_ca_system_score_gemma":0.00013448334,"threshold_uncertainty_score":0.0023715496},"labels":[],"label_agreement":null},{"id":"W4393192493","doi":"10.1099/mgen.0.001217","title":"Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Otolaryngology and Infectious Diseases","field":"Medicine","cited_by":15,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McGill University","funders":"Health Research Board","keywords":"Fusobacterium nucleatum; Biology; Bacterial adhesin; Virulence; Gene; Microbiology; Genetics; Genome; Subspecies; Intergenic region; Phylogenetic tree; Horizontal gene transfer; Porphyromonas gingivalis; Bacteria","score_opus":0.009398737099770887,"score_gpt":0.2219321202604512,"score_spread":0.21253338316068032,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4393192493","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99900824,0.00015025992,0.00020266554,0.0000115992825,0.0000024950548,0.000010207339,0.00040366597,0.0000057861416,0.0002051703],"genre_scores_gemma":[0.99827397,0.00011416235,0.00047287648,0.000016695336,0.0000037158593,0.000013094564,0.00086927536,0.0000028944992,0.0002333447],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9998491,0.000009821979,0.000018308236,0.000048069996,0.000037225687,0.00003742553],"domain_scores_gemma":[0.9998753,0.000020730513,0.0000385154,0.000016307857,0.000023625098,0.00002556461],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000101690806,0.00028948055,0.00027485346,0.00066082145,0.00034930938,0.00027558662,0.00011077288,0.00025362603,0.0006430908],"category_scores_gemma":[0.00037299702,0.00011525252,0.00018006594,0.0006743865,0.00014203557,0.00018851,0.00031451322,0.0001371374,0.000120794684],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00059378514,0.00008328138,0.18374957,0.00008477434,0.00004485471,0.0010015548,0.00072956027,0.00008636857,0.80248743,0.000059152633,0.00014666156,0.010933037],"study_design_scores_gemma":[0.000013175768,0.0003653817,0.9574847,0.000012821842,0.00007978749,0.0039886152,0.0010688589,0.00036126853,0.035179526,0.00009030809,0.0013418403,0.000013807534],"about_ca_topic_score_codex":0.0032836758,"about_ca_topic_score_gemma":0.0029865466,"teacher_disagreement_score":0.0032836758,"about_ca_system_score_codex":0.00011351048,"about_ca_system_score_gemma":0.00011356332,"threshold_uncertainty_score":0.0065291524},"labels":[],"label_agreement":null},{"id":"W4396707131","doi":"10.1099/mgen.0.001241","title":"Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Wheat and Barley Genetics and Pathology","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement; Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail; Agence Nationale de la Recherche; University of Alberta; Washington State University","keywords":"Biology; Host (biology); Fungal pathogen; Population; Pathogen; Crop; Ecology; Genetics","score_opus":0.014185070470649278,"score_gpt":0.21993556887752622,"score_spread":0.20575049840687692,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4396707131","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9993789,0.000050425606,0.00027147983,0.000009609899,0.000001275637,0.0000019792644,0.00009224567,0.000005654802,0.0001884004],"genre_scores_gemma":[0.99927527,0.000025044828,0.00020648295,0.000012327913,0.000002031536,0.0000038655307,0.0002375965,0.00000535672,0.0002320003],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9997515,0.000042280975,0.000009333813,0.000118695556,0.000026612164,0.000051623818],"domain_scores_gemma":[0.99963427,0.00009016862,0.00012611589,0.00004387165,0.00005118253,0.000054413937],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00030838806,0.00014980568,0.00022169037,0.00071557367,0.000278306,0.00047246108,0.00020374086,0.00025120212,0.0009250949],"category_scores_gemma":[0.00041423773,0.0001047846,0.00022094844,0.0003915665,0.00020584346,0.00019963183,0.0002967205,0.000337734,0.00014965335],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00053226616,0.00010022124,0.44934806,0.000037057995,0.00016647363,0.0002494567,0.0013528275,0.0009822923,0.53023744,0.00034108694,0.00018038672,0.016472418],"study_design_scores_gemma":[0.0000030603178,0.000038964128,0.99774927,0.0000015515801,0.000010688387,0.000079576545,0.00011418355,0.00055737264,0.0011256558,0.000038160862,0.0002762403,0.000005333102],"about_ca_topic_score_codex":0.006226961,"about_ca_topic_score_gemma":0.008919684,"teacher_disagreement_score":0.006226961,"about_ca_system_score_codex":0.00060061424,"about_ca_system_score_gemma":0.00020216085,"threshold_uncertainty_score":0.012381434},"labels":[],"label_agreement":null},{"id":"W4396856616","doi":"10.1099/mgen.0.001251","title":"Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Oral microbiology and periodontitis research","field":"Dentistry","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of British Columbia","funders":"University of Bradford","keywords":"Microbiome; Antibiotic resistance; Oral Microbiome; Disease; Resistance (ecology); Antibiotics; Biology; Host (biology); Human microbiome; Metagenomics; Ecology; Medicine; Microbiology; Genetics; Gene","score_opus":0.022646314953016205,"score_gpt":0.2929013130469631,"score_spread":0.2702549980939469,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4396856616","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9381136,0.03764465,0.01399294,0.00088805705,0.00008802672,0.000033122564,0.0035399185,0.00005524749,0.0056443308],"genre_scores_gemma":[0.96223503,0.019138893,0.014791207,0.00032150227,0.00006580823,0.000031991414,0.0021901492,0.000029199104,0.0011961526],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9996915,0.000121646226,0.000024183464,0.00007273339,0.000050396084,0.000039597515],"domain_scores_gemma":[0.9996014,0.00017161391,0.000097580305,0.00003703116,0.00005714326,0.00003520172],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007860164,0.00025698953,0.00048087488,0.001533972,0.0004404803,0.001018712,0.00023135023,0.0004831071,0.0014692483],"category_scores_gemma":[0.0026535392,0.00023201933,0.0003625318,0.0018437656,0.00034554512,0.0005987378,0.00067191914,0.00047986614,0.00044529972],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0005324736,0.00010099415,0.77507466,0.0013912133,0.00075070624,0.00086583436,0.00226979,0.0019407959,0.021882903,0.0018656391,0.002512529,0.19081248],"study_design_scores_gemma":[0.000011742438,0.00019073434,0.9556817,0.00064864545,0.00046727265,0.0024352907,0.00303468,0.0031683352,0.0026195564,0.0059825443,0.025715983,0.000043584037],"about_ca_topic_score_codex":0.003723622,"about_ca_topic_score_gemma":0.008202863,"teacher_disagreement_score":0.003723622,"about_ca_system_score_codex":0.00024636107,"about_ca_system_score_gemma":0.00034171063,"threshold_uncertainty_score":0.00740391},"labels":[],"label_agreement":null},{"id":"W4398777841","doi":"10.1099/mgen.0.001249","title":"Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"SARS-CoV-2 detection and testing","field":"Medicine","cited_by":16,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Western University; University of Waterloo; Environment and Climate Change Canada; McGill University","funders":"National Institute of General Medical Sciences; Canadian Institutes of Health Research; Compute Canada","keywords":"Biology; Lineage (genetic); Computational biology; Genetic diversity; Genome; Reference genome; Genetics; DNA sequencing; Population; Genomics; Whole genome sequencing; Evolutionary biology; Gene","score_opus":0.19170738493440226,"score_gpt":0.41089971479052884,"score_spread":0.21919232985612658,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4398777841","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.97505367,0.0006374832,0.018689761,0.00096386886,0.00013142545,0.00017870875,0.00096751907,0.00047372552,0.0029037783],"genre_scores_gemma":[0.9583433,0.00037851857,0.038497288,0.00035544307,0.000032832206,0.00026332188,0.0015428512,0.00009276354,0.00049375166],"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","domain_scores_codex":[0.9985942,0.000824248,0.00011457827,0.00016222142,0.0001763024,0.00012836885],"domain_scores_gemma":[0.9785718,0.01825668,0.0005658436,0.0006831964,0.0014290718,0.0004933792],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0055536767,0.0014884498,0.0017016854,0.0012455134,0.0010393715,0.0018182253,0.0021047967,0.0024865167,0.0009884494],"category_scores_gemma":[0.01745021,0.00083258946,0.00188472,0.0011158378,0.0011306567,0.0013490559,0.0015148303,0.0021911552,0.0001289439],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00021175262,0.00014841351,0.0071626008,0.000081714476,0.000097964454,0.00004933955,0.00005144313,0.98777467,0.00026536357,0.0006711939,0.00023438409,0.0032512394],"study_design_scores_gemma":[0.00003567808,0.00007443194,0.0006414018,0.000013435743,0.00002402533,0.000008737746,0.00004374639,0.9984861,0.00021833867,0.00030744885,0.0001364227,0.000010201497],"about_ca_topic_score_codex":0.039472032,"about_ca_topic_score_gemma":0.02659004,"teacher_disagreement_score":0.039472032,"about_ca_system_score_codex":0.0018279394,"about_ca_system_score_gemma":0.00256039,"threshold_uncertainty_score":0.078484595},"labels":[],"label_agreement":null},{"id":"W4399323991","doi":"10.1099/mgen.0.001254","title":"How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":101,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Institute of Infection and Immunity; National Health and Medical Research Council; Garnett Passe and Rodney Williams Memorial Foundation; National Institute of Diabetes and Digestive and Kidney Diseases; Medical Research Council; National Institutes of Health","keywords":"Polishing; Nanopore sequencing; Nanopore; Computer science; Nanotechnology; Optics; Physics; Materials science; Mechanical engineering; Engineering; Genome; Chemistry","score_opus":0.011313791049799286,"score_gpt":0.2178649977428809,"score_spread":0.2065512066930816,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4399323991","genre_codex":"methods","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.13503024,0.032809217,0.7262205,0.019307857,0.003687325,0.00048727027,0.012070688,0.05300769,0.017379172],"genre_scores_gemma":[0.1825635,0.005566411,0.7762338,0.007067398,0.00030639183,0.00042012645,0.008817427,0.010340355,0.008684576],"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.99459654,0.0015666586,0.00066670484,0.0009935257,0.0017678845,0.00040873134],"domain_scores_gemma":[0.9905911,0.0038305384,0.0007853093,0.0015396372,0.0025876793,0.0006657417],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.008138989,0.0012551879,0.0015575732,0.0017675135,0.0013783147,0.004243856,0.0020926262,0.002588591,0.006444468],"category_scores_gemma":[0.032365672,0.0016439792,0.0013883865,0.0011325054,0.0010452708,0.0050138365,0.0024799174,0.0036121001,0.009234042],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0018264538,0.00014038882,0.019019194,0.005461986,0.0007011787,0.0006746575,0.002192698,0.003877145,0.48483783,0.008423502,0.0653919,0.40745306],"study_design_scores_gemma":[0.00012315217,0.000526639,0.013718196,0.0017735817,0.00050248747,0.0012984108,0.0010790654,0.015526846,0.65930384,0.021209024,0.28431407,0.00062464975],"about_ca_topic_score_codex":0.0019875225,"about_ca_topic_score_gemma":0.004736376,"teacher_disagreement_score":0.008138989,"about_ca_system_score_codex":0.0011285287,"about_ca_system_score_gemma":0.0012333661,"threshold_uncertainty_score":0.043043554},"labels":[],"label_agreement":null},{"id":"W4399537774","doi":"10.1099/mgen.0.001261","title":"Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Plant Pathogens and Fungal Diseases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"University of North Carolina at Charlotte; Agricultural Research Service; National Institute of Food and Agriculture; University of California, Riverside; Canadian Institute for Advanced Research; Division of Environmental Biology; Office of Science; U.S. Department of Agriculture; U.S. Department of Energy; National Institutes of Health; National Science Foundation","keywords":"Effector; Biology; Diversity (politics); Symbiosis; Evolutionary biology; Zoology; Ecology; Genetics; Bacteria; Cell biology; Sociology; Anthropology","score_opus":0.005931235594392583,"score_gpt":0.19328245604692357,"score_spread":0.187351220452531,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4399537774","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9983259,0.0002182795,0.00035036958,0.000013095508,0.0000019978083,0.00001061326,0.00077836524,0.000011892807,0.00028958757],"genre_scores_gemma":[0.99716526,0.00022809907,0.0009919961,0.000022652448,0.0000035694154,0.000018982939,0.0012874786,0.000007883754,0.00027406917],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9997063,0.000019284427,0.00004014194,0.00012444037,0.00006078873,0.00004894038],"domain_scores_gemma":[0.99956423,0.00007614427,0.00014694518,0.000028539074,0.00010169968,0.00008254591],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00018647488,0.0003056635,0.00025952817,0.0012509873,0.0002944727,0.00060668687,0.00022346771,0.00040781873,0.00055538677],"category_scores_gemma":[0.0005122862,0.00018906244,0.00026353213,0.0008342719,0.00026379834,0.0003652239,0.00058305863,0.0002444849,0.0001898917],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00036699857,0.00006066711,0.1146386,0.00018530262,0.000060354563,0.00029244277,0.0010001987,0.0001450263,0.87430996,0.00008570197,0.000065056636,0.008789724],"study_design_scores_gemma":[0.00001137143,0.00027416518,0.9559059,0.000027613252,0.000087399356,0.0014630135,0.0011733869,0.0004700511,0.038838077,0.00007111938,0.0016522408,0.00002562105],"about_ca_topic_score_codex":0.0014017406,"about_ca_topic_score_gemma":0.001745202,"teacher_disagreement_score":0.0014017406,"about_ca_system_score_codex":0.00013992745,"about_ca_system_score_gemma":0.00014226096,"threshold_uncertainty_score":0.0027871132},"labels":[],"label_agreement":null},{"id":"W4399538170","doi":"10.1099/mgen.0.001260","title":"PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Biomedical Text Mining and Ontologies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McMaster University; Public Health Agency of Canada; Western University; Dalhousie University; Simon Fraser University","funders":"European and Developing Countries Clinical Trials Partnership; Biotechnology and Biological Sciences Research Council; U.S. National Library of Medicine; Foreign, Commonwealth and Development Office; Bill and Melinda Gates Foundation; European Commission; Medical Research Council; Directorate for Biological Sciences; Public Health Agency; National Institutes of Health; Public Health Agency of Canada","keywords":"Quality (philosophy); Computer science; Control (management); Sequence (biology); Data quality; Information retrieval; Data science; Knowledge management; Artificial intelligence; Engineering; Biology; Operations management","score_opus":0.33853974373146933,"score_gpt":0.4206014580559228,"score_spread":0.08206171432445347,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4399538170","genre_codex":"methods","genre_gemma":"methods","domain_codex":null,"domain_gemma":"reproducibility","model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":"methods","domain_candidate":"reproducibility","domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.023732305,0.0015525013,0.6540385,0.005234024,0.0029877482,0.0053029424,0.19975089,0.08362654,0.023774585],"genre_scores_gemma":[0.047734354,0.001334837,0.61866015,0.0037651851,0.0005184207,0.008209357,0.29438084,0.01707167,0.008325219],"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","domain_scores_codex":[0.96420306,0.011302476,0.009719279,0.0047165067,0.007950606,0.0021080533],"domain_scores_gemma":[0.8459331,0.04888119,0.018574417,0.056463793,0.0259402,0.004207415],"candidate_categories":["metaresearch","open_science"],"consensus_categories":[],"category_scores_codex":[0.065445945,0.0027646113,0.002263831,0.012082308,0.0035229735,0.007691872,0.004062884,0.0035280574,0.010098468],"category_scores_gemma":[0.12701876,0.0020088675,0.00260811,0.01059272,0.0036601597,0.00981439,0.012384986,0.00701912,0.0124715455],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.007904716,0.0012520337,0.047051832,0.010086365,0.00055940344,0.0018116687,0.011040049,0.008406655,0.08270133,0.116571,0.4274693,0.2851457],"study_design_scores_gemma":[0.0002921635,0.00029647132,0.012770612,0.0039024218,0.00022064826,0.00057717273,0.001731808,0.0064570936,0.06819549,0.035971988,0.86900645,0.0005777455],"about_ca_topic_score_codex":0.008135876,"about_ca_topic_score_gemma":0.007988164,"teacher_disagreement_score":0.9959371,"about_ca_system_score_codex":0.00499786,"about_ca_system_score_gemma":0.016079621,"threshold_uncertainty_score":0.34611535},"labels":[],"label_agreement":null},{"id":"W4399805565","doi":"10.1099/mgen.0.001257","title":"Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"North York General Hospital; Public Health Agency of Canada","funders":"Public Health Agency of Canada","keywords":"Plasmid; Biology; Klebsiella pneumoniae; Horizontal gene transfer; Mobile genetic elements; Genome; Genetics; Transposable element; Gene; Microbiology; Virology; Escherichia coli","score_opus":0.01199855918142465,"score_gpt":0.22813803623949255,"score_spread":0.2161394770580679,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4399805565","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.98641276,0.0018049926,0.00037301486,0.00017623353,0.000015661079,0.00011142099,0.008989946,0.000036464844,0.0020795984],"genre_scores_gemma":[0.98957026,0.0017720944,0.0008478529,0.00014363448,0.0000070947244,0.000027970194,0.0056257807,0.000013437305,0.0019918447],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99927443,0.000014719306,0.000032443357,0.00015797364,0.00033381997,0.00018670449],"domain_scores_gemma":[0.99840707,0.000048883903,0.0001962328,0.000030131325,0.0009196611,0.00039800347],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00031050688,0.0005973504,0.0004323608,0.0038028876,0.0022343444,0.0017437389,0.00088759686,0.0004338537,0.0014451782],"category_scores_gemma":[0.0010252935,0.00038424318,0.00041314118,0.0049906047,0.001008737,0.00021873308,0.0007072786,0.00048789408,0.00021520269],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00038737245,0.000074948985,0.96335584,0.00018163194,0.0000812974,0.00036842274,0.0015889102,0.00063857844,0.012035253,0.00024264766,0.001670892,0.019374136],"study_design_scores_gemma":[0.000008276056,0.000043165717,0.9956671,0.000036801262,0.00003362737,0.00015630912,0.001184061,0.00032972824,0.00043385854,0.00001632632,0.002073851,0.000016976182],"about_ca_topic_score_codex":0.993339,"about_ca_topic_score_gemma":0.9948054,"teacher_disagreement_score":0.021379733,"about_ca_system_score_codex":0.021379733,"about_ca_system_score_gemma":0.0360976,"threshold_uncertainty_score":0.15512156},"labels":[],"label_agreement":null},{"id":"W4401252041","doi":"10.1099/mgen.0.001276","title":"Whole-genome sequencing of Western Canadian Borrelia spp. collected from diverse tick and animal hosts reveals short-lived local genotypes interspersed with longer-lived continental genotypes","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Vector-borne infectious diseases","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"University of British Columbia; Simon Fraser University; BC Centre for Disease Control; University of Manitoba; University of Regina","funders":"Natural Sciences and Engineering Research Council of Canada; Public Health Agency; Public Health Agency of Canada","keywords":"Biology; Borrelia; Tick; Borrelia burgdorferi; Multilocus sequence typing; Ixodes; Lyme disease; Sensu; Zoology; Genotype; Genetics; Virology; Gene","score_opus":0.013207343596873677,"score_gpt":0.21644172273752948,"score_spread":0.2032343791406558,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4401252041","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9777469,0.0014893516,0.0008296118,0.000118280506,0.000013012959,0.00006409853,0.016995246,0.000035761776,0.0027077456],"genre_scores_gemma":[0.95279866,0.0024659836,0.005535094,0.00021223274,0.0000080939135,0.00004499628,0.034552697,0.000030204006,0.0043519973],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9997179,0.000009550518,0.000011683521,0.000063887295,0.000117986434,0.00007894319],"domain_scores_gemma":[0.9995627,0.000023588538,0.000074052856,0.000017803899,0.000247109,0.000074750336],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00019099956,0.00036328845,0.0002543142,0.001730214,0.0012042377,0.00071451947,0.00022743618,0.00020070789,0.0007784995],"category_scores_gemma":[0.0004959917,0.0001641144,0.0003401181,0.0032244253,0.0002854899,0.00011786007,0.00037800928,0.00029651067,0.00021844816],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0006332781,0.00011720769,0.6131598,0.0006668568,0.0003633729,0.0008602419,0.004425043,0.0012418906,0.2868241,0.00040806519,0.0047242567,0.086575955],"study_design_scores_gemma":[0.0000052880387,0.000032181102,0.99058086,0.000026685639,0.000054624565,0.00017454839,0.0008295422,0.00018813413,0.0020557789,0.000020633888,0.0060235225,0.00000832288],"about_ca_topic_score_codex":0.87919724,"about_ca_topic_score_gemma":0.9642373,"teacher_disagreement_score":0.12080276,"about_ca_system_score_codex":0.0035349305,"about_ca_system_score_gemma":0.006033459,"threshold_uncertainty_score":0.24302834},"labels":[],"label_agreement":null},{"id":"W4403393007","doi":"10.1099/mgen.0.001293","title":"The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"University of Calgary; AIDS Vancouver; Mila - Quebec Artificial Intelligence Institute; Genome Canada; Michael Smith Health Research BC; Sunnybrook Health Science Centre; BC Centre for Disease Control; Women and Children’s Health Research Institute; Ontario Genomics; University of Alberta; Indoc Research; Université de Montréal; McGill Genome Centre; University of Toronto; Western University; McGill University; Simon Fraser University; Public Health Agency of Canada; Ontario Institute for Cancer Research; University of British Columbia; Montreal Heart Institute","funders":"National Cancer Institute; Canadian Institutes of Health Research; Institut de Valorisation des Données; Fonds de Recherche du Québec - Santé; Michael Smith Health Research BC; Alliance de recherche numérique du Canada; Genome Alberta; Public Health Agency of Canada; Simon Fraser University; Government of Ontario; Genome Canada; National Institutes of Health; Ontario Genomics; Government of Canada; Public Health Agency; Innovation, Science and Economic Development Canada; Canarie","keywords":"Data sharing; Pandemic; Interoperability; Big data; Suite; Genomics; Data access; Computer science; Data science; World Wide Web; Genome; Coronavirus disease 2019 (COVID-19); Database; Biology; Political science; Medicine; Data mining; Genetics","score_opus":0.13044695550893884,"score_gpt":0.39583238429948253,"score_spread":0.2653854287905437,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4403393007","genre_codex":"dataset","genre_gemma":"software","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"software","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.0037649483,0.0011799071,0.023367716,0.0055398024,0.00069532247,0.00067517377,0.8162709,0.04369985,0.10480632],"genre_scores_gemma":[0.02451197,0.0025697243,0.092927575,0.003301428,0.00028820112,0.0006507391,0.81812894,0.015136057,0.042485364],"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","domain_scores_codex":[0.9960413,0.00041116157,0.00028139478,0.00057250436,0.0020665464,0.0006271591],"domain_scores_gemma":[0.9848844,0.0023236007,0.0005643513,0.0035101543,0.005177789,0.0035396707],"candidate_categories":["open_science"],"consensus_categories":[],"category_scores_codex":[0.005383679,0.0013770111,0.0009875525,0.0072387033,0.0040313634,0.0070625013,0.0036038358,0.0016943509,0.075461075],"category_scores_gemma":[0.021000518,0.0010677722,0.0011240446,0.0118346205,0.0014470697,0.005267449,0.00837648,0.0023979442,0.035447527],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_system_candidate":true,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00026295643,0.00003598497,0.0028905242,0.00048946164,0.000036321722,0.00020965512,0.0008812234,0.00062757055,0.0012367193,0.012416551,0.9242038,0.056709267],"study_design_scores_gemma":[0.00004333607,0.000007421235,0.0024986083,0.00019368259,0.000010427084,0.00004571543,0.00032298613,0.0005998247,0.00068714254,0.0039112233,0.9915953,0.000084227446],"about_ca_topic_score_codex":0.7835557,"about_ca_topic_score_gemma":0.8251986,"teacher_disagreement_score":0.9963962,"about_ca_system_score_codex":0.013452623,"about_ca_system_score_gemma":0.054393087,"threshold_uncertainty_score":0.43543798},"labels":[],"label_agreement":null},{"id":"W4403600184","doi":"10.1099/mgen.0.001308","title":"AMRColab – a user-friendly antimicrobial resistance detection and visualization tool","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial Identification and Susceptibility Testing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Simon Fraser University","funders":"Ministry of Higher Education, Malaysia","keywords":"Visualization; User interface; Public health; Modular design; Interface (matter); Data science; Computer science; World Wide Web; Medicine; Data mining; Pathology","score_opus":0.006941000369148651,"score_gpt":0.23667288015914242,"score_spread":0.22973187978999376,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4403600184","genre_codex":"software","genre_gemma":"software","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"software","genre_consensus":"software","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.015972916,0.0021173025,0.2508764,0.0018130154,0.00054883875,0.0006129218,0.021636462,0.6935559,0.0128662195],"genre_scores_gemma":[0.1643534,0.0025145516,0.68954897,0.003983707,0.00041946865,0.0023710006,0.0602527,0.05629594,0.020260166],"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","domain_scores_codex":[0.998638,0.00032348366,0.000108053886,0.00024976552,0.00051314407,0.0001675344],"domain_scores_gemma":[0.997138,0.001364091,0.00026163942,0.0003290801,0.00057857705,0.00032865547],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0025388747,0.002387124,0.0011580862,0.0031267786,0.00058231864,0.0025718086,0.002695334,0.0015920814,0.02029716],"category_scores_gemma":[0.0065631145,0.0008683955,0.0019218654,0.0010212269,0.00040375435,0.0026177485,0.0033214428,0.0018841209,0.010458284],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0032470948,0.0005537539,0.0089895055,0.003580409,0.00058363815,0.0017392756,0.0019477534,0.0053012315,0.06559542,0.009357525,0.55076885,0.34833556],"study_design_scores_gemma":[0.0009915115,0.00052460836,0.014560279,0.001179576,0.00028499268,0.0025147507,0.00055655,0.15512866,0.070485,0.01933431,0.73365575,0.00078397256],"about_ca_topic_score_codex":0.002774882,"about_ca_topic_score_gemma":0.0031328753,"teacher_disagreement_score":0.02029716,"about_ca_system_score_codex":0.00050994434,"about_ca_system_score_gemma":0.0011651686,"threshold_uncertainty_score":0.06790078},"labels":[],"label_agreement":null},{"id":"W4403601020","doi":"10.1099/mgen.0.001294","title":"Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae","year":2024,"lang":"en","type":"review","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":18,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McMaster University","funders":"European Commission; Joint Programming Initiative on Antimicrobial Resistance; Medical Research Council; National Institute for Health and Care Research; Bill and Melinda Gates Foundation","keywords":"Biology; Klebsiella pneumoniae; Genetics; Gene; Genotyping; Plasmid; Genome; Allele; Phylogenetic tree; Genotype; Escherichia coli","score_opus":0.04638806497879486,"score_gpt":0.28270535827197363,"score_spread":0.23631729329317877,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4403601020","genre_codex":"empirical","genre_gemma":"review","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"review","genre_consensus":null,"domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9943632,0.0020565458,0.0014068872,0.000059848666,0.00000789901,0.000023355791,0.001242324,0.000022114147,0.0008178069],"genre_scores_gemma":[0.99058247,0.0012922875,0.0044214213,0.000037474478,0.000008467014,0.00002011895,0.003066725,0.000019282408,0.0005516589],"study_design_codex":"observational","study_design_gemma":"not_applicable","domain_scores_codex":[0.9986143,0.00024725837,0.0003110414,0.00035824676,0.00032701166,0.00014211696],"domain_scores_gemma":[0.99832314,0.00047081787,0.00046521286,0.00019162911,0.00040376457,0.00014541965],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00097466627,0.00023392384,0.0003120914,0.0028225968,0.0003407781,0.0011311377,0.00033243943,0.00044352087,0.00039450004],"category_scores_gemma":[0.0021622211,0.00020710992,0.0005633662,0.0020299186,0.0003183226,0.00047854419,0.00040994305,0.00035166414,0.00039301376],"study_design_candidate":"not_applicable","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00042920458,0.00006558931,0.53753346,0.0005003755,0.00012984294,0.000642327,0.0016937184,0.0005607492,0.40346318,0.00024914194,0.00024637452,0.054485943],"study_design_scores_gemma":[0.0000045536426,0.00020256445,0.94296426,0.00008069631,0.00013933075,0.0033599422,0.0011783366,0.00082456286,0.045364402,0.00018642168,0.0056579597,0.000037045873],"about_ca_topic_score_codex":0.0034617418,"about_ca_topic_score_gemma":0.0040362924,"teacher_disagreement_score":0.0034617418,"about_ca_system_score_codex":0.0003551612,"about_ca_system_score_gemma":0.00041769847,"threshold_uncertainty_score":0.006883204},"labels":[],"label_agreement":null},{"id":"W4403761062","doi":"10.1099/mgen.0.001306","title":"Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using Methylohalobius crimeensis","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial metabolism and enzyme function","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; International Microbiome Centre, University of Calgary; Genome Canada","keywords":"Ethylene; Gene cluster; Gene; Biology; Methane monooxygenase; Bacteria; Genome; Proteomics; Gene expression; Homology (biology); Genetics; Biochemistry","score_opus":0.07037967798328132,"score_gpt":0.3101542516905651,"score_spread":0.23977457370728378,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4403761062","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99856263,0.00027574744,0.00033533009,0.000028781342,0.0000029633527,0.000011367104,0.00045326434,0.000008045539,0.0003218911],"genre_scores_gemma":[0.99337137,0.0005098627,0.0029347704,0.00003810929,0.000007339585,0.000047376423,0.0021575552,0.000012943583,0.00092061126],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9998908,0.000010701975,0.000009781165,0.000037987847,0.000030984826,0.000019719455],"domain_scores_gemma":[0.9999069,0.000019106754,0.000019606881,0.0000069340786,0.000021246364,0.000026314188],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00012043664,0.0003435929,0.00034394243,0.000309205,0.0002241166,0.0002917645,0.0002790933,0.00027478902,0.00025097755],"category_scores_gemma":[0.00013578375,0.00016636636,0.00042837893,0.00043958492,0.00017452719,0.00021940545,0.0003761736,0.00037615298,0.00014509697],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00007565183,0.000024747565,0.0007118818,0.000040205636,0.0000039684523,0.00002708952,0.00005249022,0.000032023956,0.99842346,0.000011119256,0.0000036381784,0.0005936489],"study_design_scores_gemma":[0.000034049313,0.00089004915,0.32884985,0.000025098061,0.000099435856,0.0014175619,0.0010888333,0.003131114,0.66172916,0.00012556823,0.0025661092,0.000043140335],"about_ca_topic_score_codex":0.0027579751,"about_ca_topic_score_gemma":0.0030067533,"teacher_disagreement_score":0.0027579751,"about_ca_system_score_codex":0.000259964,"about_ca_system_score_gemma":0.00020742256,"threshold_uncertainty_score":0.005483806},"labels":[],"label_agreement":null},{"id":"W4404060840","doi":"10.1099/mgen.0.001319","title":"Genomic diversity of Campylobacter jejuni and Campylobacter coli isolates recovered from human and poultry in Australia and New Zealand, 2017 to 2019","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Salmonella and Campylobacter epidemiology","field":"Agricultural and Biological Sciences","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Agriculture and Agri-Food Canada","funders":"National Health and Medical Research Council; Agrifutures Australia; Department of Health and Aged Care, Australian Government; ACT Health; Queensland Health","keywords":"Campylobacter; Tetracycline; Biology; Campylobacter jejuni; Human pathogen; Genotype; Genetic diversity; Pathogen; Molecular epidemiology; Multiple drug resistance; Population; Campylobacter coli; Microbiology; Veterinary medicine; Genetics; Antibiotics; Environmental health; Bacteria; Gene; Medicine","score_opus":0.038085685255640975,"score_gpt":0.24745964685315613,"score_spread":0.20937396159751515,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4404060840","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9987669,0.00015213304,0.000068765905,0.000024035455,0.0000020833384,0.000015529413,0.0005498283,0.0000016804217,0.00041909068],"genre_scores_gemma":[0.9971349,0.0002793612,0.0002915143,0.00003687214,0.000005316984,0.000023663051,0.0015417518,0.000002681013,0.0006838918],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9996519,0.00003028128,0.00003832362,0.00010476879,0.00011827302,0.000056494166],"domain_scores_gemma":[0.9996044,0.00003782177,0.000121541365,0.000023424036,0.000120364224,0.00009246494],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002753169,0.0002307816,0.000251371,0.0015854277,0.0004266109,0.00051847665,0.00019051411,0.00025605207,0.0007877203],"category_scores_gemma":[0.00077410927,0.00017902849,0.00028104254,0.0013234244,0.0005003957,0.00022899566,0.000539219,0.00020706016,0.0001993623],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0003558624,0.000061721956,0.9382387,0.00013041614,0.00008406338,0.000924315,0.0041160784,0.000113951304,0.04200832,0.000048206373,0.00030826856,0.013610173],"study_design_scores_gemma":[0.000002516735,0.000057199835,0.9980788,0.000007219371,0.000011554788,0.00035889033,0.0006701668,0.000038531172,0.00022424197,0.0000050307226,0.00054339913,0.0000024161095],"about_ca_topic_score_codex":0.117219105,"about_ca_topic_score_gemma":0.13705139,"teacher_disagreement_score":0.117219105,"about_ca_system_score_codex":0.00073273864,"about_ca_system_score_gemma":0.0005887849,"threshold_uncertainty_score":0.23307359},"labels":[],"label_agreement":null},{"id":"W4404413012","doi":"10.1099/mgen.0.001321","title":"Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales–Entomoplasmatales clade within the class Mollicutes","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal","funders":"Academia Sinica; Canadian Patient Safety Institute","keywords":"Biology; Clade; Genome; Mollicutes; Phylogenetic tree; Phylogenetics; Taxonomy (biology); Taxonomic rank; Evolutionary biology; Spiroplasma; Gene; Genome size; Genetics; Zoology; Taxon; Ecology; Bacteria","score_opus":0.026424453559911545,"score_gpt":0.24404562070651584,"score_spread":0.2176211671466043,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4404413012","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9926196,0.0010550836,0.0047751334,0.00010907968,0.00001071344,0.00004815794,0.0005449243,0.000028994675,0.00080830057],"genre_scores_gemma":[0.9515126,0.0013163626,0.044649836,0.00007087506,0.00001817015,0.0000484408,0.0017187364,0.000050165094,0.0006148487],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9994831,0.00011758381,0.00004631889,0.00012549531,0.00014078553,0.00008654341],"domain_scores_gemma":[0.99918514,0.0002939385,0.00015017462,0.00007352935,0.00019781617,0.00009935871],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00074467127,0.00038602698,0.0005061694,0.0020188612,0.0009767406,0.0007938153,0.0003360781,0.0007222294,0.00037031033],"category_scores_gemma":[0.0015306917,0.00013066348,0.0005424682,0.0026127023,0.00046683094,0.00046232826,0.00074059103,0.0005027947,0.0002796697],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0008178912,0.0007566956,0.43323058,0.0012683171,0.00020178538,0.016307153,0.00794167,0.0059626885,0.41928473,0.0015349418,0.0019045734,0.11078895],"study_design_scores_gemma":[0.000045509478,0.0011705313,0.7105136,0.00049145945,0.0004803853,0.02001878,0.017891362,0.04406381,0.1731987,0.0031047203,0.028823944,0.00019715114],"about_ca_topic_score_codex":0.0032410182,"about_ca_topic_score_gemma":0.0053887474,"teacher_disagreement_score":0.0032410182,"about_ca_system_score_codex":0.00026184882,"about_ca_system_score_gemma":0.00027899913,"threshold_uncertainty_score":0.006444335},"labels":[],"label_agreement":null},{"id":"W4404536517","doi":"10.1099/mgen.0.001324","title":"Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation","year":2024,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":7,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Toronto","funders":"Canada Research Chairs; Genome Canada","keywords":"Biology; Synteny; Evolutionary biology; Genome; Genetics; Gene","score_opus":0.00941625209328846,"score_gpt":0.20412655610042116,"score_spread":0.19471030400713268,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4404536517","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9917293,0.0016888948,0.0032989974,0.00015849811,0.000008290764,0.000020590936,0.0015176669,0.00006392407,0.0015138469],"genre_scores_gemma":[0.9853234,0.0020543619,0.007163517,0.00012715317,0.000012768911,0.000026348342,0.0042252177,0.000042787982,0.0010244113],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99984956,0.000014513791,0.000011527138,0.00005025157,0.00003558435,0.000038429214],"domain_scores_gemma":[0.99981683,0.000035005873,0.000042359858,0.000022460728,0.000043121945,0.000040215196],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00020733538,0.00048414618,0.00031442297,0.0009812616,0.00024294894,0.0005345672,0.00021323493,0.000366668,0.0006621169],"category_scores_gemma":[0.00032686617,0.00017410767,0.00031715818,0.0011921619,0.00014028334,0.0005514188,0.0005739768,0.00042428542,0.0002114982],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00011613727,0.000031491094,0.009642472,0.0001001436,0.0000181247,0.0001038637,0.0001283238,0.00022101197,0.978225,0.00019063674,0.000051975723,0.011170783],"study_design_scores_gemma":[0.000022578872,0.00045358881,0.6951674,0.00012044518,0.0002064334,0.0017582483,0.0016692308,0.006937189,0.27293372,0.0012073079,0.019475594,0.000048204056],"about_ca_topic_score_codex":0.0013081298,"about_ca_topic_score_gemma":0.0019422929,"teacher_disagreement_score":0.0013081298,"about_ca_system_score_codex":0.0002777713,"about_ca_system_score_gemma":0.00030464758,"threshold_uncertainty_score":0.002601087},"labels":[],"label_agreement":null},{"id":"W4407743990","doi":"10.1099/mgen.0.001368","title":"Genomic diversity and evolutionary patterns of Edwardsiella ictaluri affecting farmed striped catfish (Pangasianodon hypophthalmus) in Vietnam over 20 years","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Aquaculture disease management and microbiota","field":"Immunology and Microbiology","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":false,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"","funders":"Department of Health and Social Care; International Development Research Centre; Government of the United Kingdom","keywords":"Biology; Genome; Virulence; Genetics; Edwardsiella ictaluri; Plasmid; Gene; Catfish; Genome evolution; Whole genome sequencing; Comparative genomics; Genomics; Fishery","score_opus":0.0075338132500965445,"score_gpt":0.20927318610270132,"score_spread":0.20173937285260476,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4407743990","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99937975,0.00011578045,0.000044469085,0.000011187787,5.760091e-7,0.0000035953874,0.0002801095,0.0000011557195,0.0001632836],"genre_scores_gemma":[0.9984124,0.00018027189,0.00015272303,0.000014846838,0.0000013840576,0.000007938335,0.0008733902,0.0000016424261,0.00035537832],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9998233,0.000014126865,0.000016909096,0.00007944374,0.00002642278,0.00003979131],"domain_scores_gemma":[0.9996557,0.000050978684,0.00012918233,0.000016072545,0.000073872674,0.00007420843],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00015857088,0.00015183268,0.00017255281,0.00092813984,0.00020076819,0.0003866507,0.00013011666,0.00018692027,0.0004833291],"category_scores_gemma":[0.0003913877,0.00011093229,0.00019915008,0.0008547071,0.00023436229,0.00018527909,0.00029738917,0.00015013402,0.000076633296],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00028993492,0.000051408075,0.85524666,0.0001271878,0.00009581897,0.0013604932,0.0026571085,0.00038581877,0.12847629,0.000084986896,0.00011500349,0.01110925],"study_design_scores_gemma":[0.0000017102499,0.000049820166,0.9975478,0.000008956626,0.000012307448,0.00036372803,0.0008330059,0.000099536766,0.00067084876,0.000011460081,0.00039787812,0.0000028974544],"about_ca_topic_score_codex":0.010033969,"about_ca_topic_score_gemma":0.01601345,"teacher_disagreement_score":0.010033969,"about_ca_system_score_codex":0.00038871128,"about_ca_system_score_gemma":0.00025857825,"threshold_uncertainty_score":0.019951105},"labels":[],"label_agreement":null},{"id":"W4409499435","doi":"10.1099/mgen.0.001380","title":"Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host–microbe interactions","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Queen's University","funders":"Centre National de la Recherche Scientifique; Natural Sciences and Engineering Research Council of Canada; Mitacs; Queen's University; Agence Nationale de la Recherche","keywords":"Phylum; Biology; Evolutionary biology; Phylogenetics; Genetics; Bacteria; Gene","score_opus":0.010234258853627276,"score_gpt":0.2402454949686427,"score_spread":0.23001123611501542,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4409499435","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9965701,0.0010025469,0.0012953057,0.000032909553,0.0000038634353,0.0000146534,0.00020991698,0.00002593062,0.00084469415],"genre_scores_gemma":[0.9959682,0.0003774749,0.002463416,0.000037563983,0.000005628558,0.000012662965,0.00085417076,0.000009034669,0.0002719209],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99957484,0.00005964624,0.000032185697,0.00016308624,0.00009318233,0.00007712329],"domain_scores_gemma":[0.99946266,0.000087956636,0.00013553079,0.00004478936,0.00014053716,0.00012841837],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00050813955,0.00022819424,0.0004945622,0.00289326,0.00079770427,0.0010375442,0.00034214044,0.00057132525,0.0011504655],"category_scores_gemma":[0.0006386653,0.00022052371,0.0004988812,0.0016802993,0.0005744759,0.0006828038,0.0008324958,0.0004383169,0.0006460675],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0006511311,0.00014890949,0.3989296,0.00028636618,0.00023552535,0.00033629723,0.0010317725,0.00057034823,0.56704867,0.0010263992,0.00018763648,0.029547445],"study_design_scores_gemma":[0.000016007409,0.0001875915,0.9858068,0.000034063723,0.00006378951,0.00089467934,0.0006699778,0.0031816312,0.0063006184,0.0005845155,0.0022298011,0.000030622858],"about_ca_topic_score_codex":0.001894237,"about_ca_topic_score_gemma":0.0026412348,"teacher_disagreement_score":0.00289326,"about_ca_system_score_codex":0.0004182116,"about_ca_system_score_gemma":0.0004001563,"threshold_uncertainty_score":0.003848672},"labels":[],"label_agreement":null},{"id":"W4410232257","doi":"10.1099/mgen.0.001386","title":"Detection of novel Plasmodium falciparum haplotypes under treatment pressure in paediatric severe malaria","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Malaria Research and Control","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Calgary","funders":"Institut Mérieux; Université de Montpellier; Fondation pour la Recherche Médicale; Agence Nationale de la Recherche; Centre National de la Recherche Scientifique; Alliance Française contre les Maladies Parasitaires","keywords":"Plasmodium falciparum; Malaria; Artesunate; Quinine; Parasite hosting; Virology; Biology; Multiplicity of infection; Immunology; Virus","score_opus":0.013979818522368653,"score_gpt":0.25034121332009246,"score_spread":0.2363613947977238,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4410232257","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9986727,0.0002357816,0.0006028196,0.000025419378,0.0000025968125,0.000010405612,0.00020608703,0.000007951303,0.00023614503],"genre_scores_gemma":[0.9985129,0.00012384419,0.0010152387,0.000020800484,0.0000050316007,0.0000118254975,0.00021178144,0.00000533949,0.000093370065],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.999574,0.00013476633,0.000028008286,0.00012178932,0.00008543857,0.00005598808],"domain_scores_gemma":[0.9990231,0.0002478992,0.0005002051,0.000057653382,0.000089776295,0.0000814252],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004871234,0.00017619744,0.0002275073,0.00037319335,0.00020772914,0.0002783832,0.00017516557,0.0002754298,0.0011516617],"category_scores_gemma":[0.0015849348,0.0001585547,0.00014624625,0.0005285597,0.0002998447,0.00018507251,0.00026014278,0.0002865381,0.00015304054],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00032859197,0.000025035353,0.9564105,0.0000781444,0.000028033988,0.00048583775,0.0006248581,0.0002936683,0.028302873,0.00007306944,0.00022700116,0.013122337],"study_design_scores_gemma":[0.000006563352,0.00018281216,0.9933622,0.000012623196,0.000018688123,0.0018033733,0.00026048298,0.00050013943,0.0030257383,0.000058944734,0.00076316646,0.000005096279],"about_ca_topic_score_codex":0.0007656257,"about_ca_topic_score_gemma":0.0012459856,"teacher_disagreement_score":0.0011516617,"about_ca_system_score_codex":0.00017204286,"about_ca_system_score_gemma":0.00013942838,"threshold_uncertainty_score":0.0038526654},"labels":[],"label_agreement":null},{"id":"W4411581593","doi":"10.1099/mgen.0.001436","title":"Comparative genomic analysis of Escherichia coli isolated from cases of bovine clinical mastitis and the dairy farm environment","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Milk Quality and Mastitis in Dairy Cows","field":"Agricultural and Biological Sciences","cited_by":2,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Université de Montréal; Health Canada; McGill University; Fonds de Recherche du Québec – Nature et Technologies; Cegep de Saint Hyacinthe","funders":"","keywords":"Mastitis; Escherichia coli; Biology; Biotechnology; Dairy cattle; Bovine milk; Microbiology; Food science; Animal science; Genetics; Gene","score_opus":0.0340730046621284,"score_gpt":0.2649962491060965,"score_spread":0.23092324444396808,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4411581593","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9987997,0.00021038862,0.00019807505,0.000019694273,0.0000041669423,0.000008917275,0.00039063842,0.000002387171,0.0003661804],"genre_scores_gemma":[0.99738294,0.00029003315,0.0005147436,0.000044384506,0.000007652411,0.000008673211,0.0015257583,0.000003903846,0.00022192804],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99959546,0.000058211088,0.000033561497,0.00010746718,0.000100739,0.00010456055],"domain_scores_gemma":[0.9996126,0.000116444,0.000115391806,0.000020918733,0.00007246229,0.00006227154],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00018912087,0.00021268569,0.00025672946,0.0016482789,0.00031755207,0.0003746131,0.00017294995,0.00037029322,0.00070905493],"category_scores_gemma":[0.00074047525,0.00014450464,0.00031113005,0.0014327978,0.0003201255,0.000116001276,0.00038631633,0.00024994262,0.00017326736],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0011694366,0.00027411195,0.5409706,0.00024216378,0.0001590213,0.0052831196,0.0014469358,0.00019706336,0.43352744,0.00010592294,0.0002625872,0.016361542],"study_design_scores_gemma":[0.0000056359463,0.0002157186,0.98845834,0.000010444694,0.00004930721,0.003411962,0.0008853424,0.00012986334,0.006126979,0.000022971197,0.0006792301,0.0000041951757],"about_ca_topic_score_codex":0.0026967188,"about_ca_topic_score_gemma":0.0030911479,"teacher_disagreement_score":0.0026967188,"about_ca_system_score_codex":0.0002041027,"about_ca_system_score_gemma":0.00015705572,"threshold_uncertainty_score":0.0053619742},"labels":[],"label_agreement":null},{"id":"W4412173166","doi":"10.1099/mgen.0.001438","title":"skDER and CiDDER: two scalable approaches for microbial genome dereplication","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McMaster University; Population Health Research Institute","funders":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences","keywords":"Scalability; Computational biology; Genome; Biology; Computer science; Genetics; Database; Gene","score_opus":0.016293618075083456,"score_gpt":0.23286433907137793,"score_spread":0.21657072099629449,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4412173166","genre_codex":"methods","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":"methods","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.033606324,0.002712035,0.48939675,0.00083130295,0.0009917091,0.0013956134,0.02674193,0.43852216,0.0058021345],"genre_scores_gemma":[0.05572605,0.0012451352,0.83127415,0.0008761539,0.00016176194,0.0020442945,0.073729016,0.03132111,0.0036222283],"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9955837,0.0006706856,0.00049875496,0.0015294862,0.001325398,0.00039200982],"domain_scores_gemma":[0.9937249,0.0019209315,0.0006129273,0.0024494668,0.00082577317,0.00046604598],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.005351336,0.003471545,0.002558109,0.00368427,0.0016702978,0.0040708473,0.0048095766,0.001930939,0.010862729],"category_scores_gemma":[0.016023463,0.0021742315,0.0038559588,0.0033815391,0.0011135776,0.004734589,0.010061673,0.0041875695,0.011400811],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.005739598,0.001047288,0.015826285,0.0057610897,0.0022980494,0.0016681683,0.003732442,0.021550596,0.1850426,0.013557148,0.18698952,0.5567872],"study_design_scores_gemma":[0.0026445398,0.0014557369,0.017087137,0.00064242096,0.0009274474,0.0024344134,0.001350671,0.36125523,0.23712736,0.039684445,0.33391014,0.0014804717],"about_ca_topic_score_codex":0.0024420016,"about_ca_topic_score_gemma":0.004115699,"teacher_disagreement_score":0.010862729,"about_ca_system_score_codex":0.001063482,"about_ca_system_score_gemma":0.0026172565,"threshold_uncertainty_score":0.03633946},"labels":[{"model":"gemma","categories":[],"domain":null,"study_design":"simulation_or_modeling","genre":"methods","about_ca_system":false,"about_ca_topic":false,"confidence":"low"},{"model":"gpt","categories":[],"domain":null,"study_design":"design_other","genre":"methods","about_ca_system":false,"about_ca_topic":false,"confidence":"high"}],"label_agreement":"split"},{"id":"W4412654900","doi":"10.1099/mgen.0.001437","title":"Vibrio cholerae lineage and pangenome diversity vary geographically across Bangladesh over 1 year","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Vibrio bacteria research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"McGill University; McGill Genome Centre","funders":"Canadian Institutes of Health Research; Fogarty International Center; National Institutes of Health; Wellcome Trust","keywords":"Vibrio cholerae; Lineage (genetic); Diversity (politics); Geography; Biology; Political science; Genetics; Bacteria","score_opus":0.007109518462243162,"score_gpt":0.25239188718455824,"score_spread":0.24528236872231507,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4412654900","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.98260766,0.001336722,0.0005248517,0.00015949659,0.000013269769,0.000027679263,0.012870372,0.000043827484,0.0024161148],"genre_scores_gemma":[0.98001087,0.0014412919,0.0008218827,0.00017629832,0.000007969508,0.000090813184,0.015937803,0.00003285863,0.0014802243],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9995023,0.000059573016,0.000059899216,0.00017484871,0.00010364641,0.0000996331],"domain_scores_gemma":[0.99917763,0.00012329067,0.0001854779,0.000070033646,0.00031929373,0.00012422424],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00040333348,0.00033805755,0.00036023802,0.0010986776,0.00049820525,0.00068637845,0.0002626124,0.00029418844,0.0020577093],"category_scores_gemma":[0.0017570307,0.00020238147,0.00026948712,0.0021387802,0.0002769674,0.00051261886,0.0007990965,0.00034581433,0.0007486167],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00077284424,0.000029669405,0.83865106,0.0005857818,0.0002399275,0.0005922644,0.0045938506,0.0007072039,0.11736986,0.00026480117,0.003189044,0.033003744],"study_design_scores_gemma":[0.000009702723,0.000085535845,0.97998536,0.000065905246,0.00006829131,0.00038160043,0.0026952242,0.0002461144,0.0025301147,0.00015490873,0.013740119,0.000037152575],"about_ca_topic_score_codex":0.014921621,"about_ca_topic_score_gemma":0.024734763,"teacher_disagreement_score":0.014921621,"about_ca_system_score_codex":0.00074201165,"about_ca_system_score_gemma":0.0005065495,"threshold_uncertainty_score":0.029669583},"labels":[],"label_agreement":null},{"id":"W4412940655","doi":"10.1099/mgen.0.001415","title":"Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Jewish General Hospital; Public Health Agency of Canada","funders":"","keywords":"Plasmid; Replicon; Biology; Genome; Whole genome sequencing; Gene; Genetics; Horizontal gene transfer; Microbiology","score_opus":0.010319258021687398,"score_gpt":0.2312264236200367,"score_spread":0.2209071655983493,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4412940655","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9893366,0.001724263,0.0003482647,0.00035560026,0.000016736754,0.00006511323,0.006208258,0.000034177025,0.0019109127],"genre_scores_gemma":[0.9944443,0.0009892611,0.00050453877,0.00016640627,0.000004903838,0.00001847758,0.0028446042,0.000010893178,0.0010166359],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9992918,0.00002176832,0.00003070457,0.00012939985,0.00029986797,0.00022647335],"domain_scores_gemma":[0.9979348,0.000060051436,0.00023067009,0.000036000652,0.0012684255,0.00047007445],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000342873,0.0004764264,0.00034228837,0.00295246,0.0019890063,0.0011859965,0.0007842641,0.00041278492,0.0013107586],"category_scores_gemma":[0.0012610406,0.00027541327,0.00041618352,0.005001262,0.00075489865,0.00024947504,0.0007435059,0.00048039015,0.0001510889],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":true,"about_ca_topic_consensus":true,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0002131606,0.000037648377,0.975902,0.00010079169,0.000055200537,0.0003469888,0.0011135931,0.00041704765,0.005419553,0.0002040657,0.0016071858,0.014582779],"study_design_scores_gemma":[0.000004707714,0.000031943902,0.9954679,0.00004186827,0.000023792816,0.00019492432,0.0013625636,0.00041405813,0.0004105545,0.000022957303,0.0020088837,0.000015870259],"about_ca_topic_score_codex":0.99366415,"about_ca_topic_score_gemma":0.9945533,"teacher_disagreement_score":0.022858901,"about_ca_system_score_codex":0.022858901,"about_ca_system_score_gemma":0.036112756,"threshold_uncertainty_score":0.16585374},"labels":[],"label_agreement":null},{"id":"W4415881079","doi":"10.1099/mgen.0.001543","title":"Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Public Health Ontario; Manitoba Health; University of Manitoba; Western University","funders":"Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Genetic diversity; Genome; Pathogen; Opportunistic pathogen; Population; Human pathogen; Phylogenetics; Population structure; Gene","score_opus":0.007833479287445896,"score_gpt":0.25301463869811425,"score_spread":0.24518115941066834,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4415881079","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.99729055,0.0001934467,0.0019660138,0.00003192566,0.0000012409644,0.000002742649,0.00008765783,0.000006599489,0.0004198729],"genre_scores_gemma":[0.9989428,0.00008248066,0.0007298662,0.000014010623,0.0000037035697,0.0000018295085,0.00015357026,0.0000029486741,0.00006878668],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.9998518,0.00004387174,0.000006614842,0.00005998895,0.000017003176,0.000020742325],"domain_scores_gemma":[0.99974185,0.000110416215,0.000068754765,0.00002735019,0.00002794236,0.000023704313],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004018157,0.00013060967,0.0001749544,0.0008062695,0.00018618032,0.00034504538,0.0001239369,0.00023020933,0.00059380266],"category_scores_gemma":[0.00076870853,0.00009325374,0.00017661137,0.0006067508,0.00025593909,0.00025775857,0.00026861342,0.00026929114,0.0001003587],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00028548503,0.00006880451,0.8153903,0.00008329389,0.00034138054,0.00041433025,0.002080291,0.008995145,0.11290885,0.0027386497,0.00032392106,0.056369536],"study_design_scores_gemma":[0.000010471556,0.000099848716,0.9832529,0.000018382503,0.00006311038,0.0003764361,0.0005106049,0.011616372,0.0012017182,0.0014783799,0.0013568394,0.000014969317],"about_ca_topic_score_codex":0.001462734,"about_ca_topic_score_gemma":0.002786454,"teacher_disagreement_score":0.001462734,"about_ca_system_score_codex":0.00018514664,"about_ca_system_score_gemma":0.00012510968,"threshold_uncertainty_score":0.0029084682},"labels":[],"label_agreement":null},{"id":"W4415928759","doi":"10.1099/mgen.0.001537","title":"Novel insights into the genome organization of Rhizobiaceae: identification of linear plasmids","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Legume Nitrogen Fixing Symbiosis","field":"Agricultural and Biological Sciences","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Calgary; Queen's University","funders":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada; Deutsche Forschungsgemeinschaft","keywords":"Extrachromosomal DNA; Replicon; Plasmid; Genome; Chromosome; Circular bacterial chromosome; T-DNA Binary system; Identification (biology)","score_opus":0.00745098289051829,"score_gpt":0.1956696988709593,"score_spread":0.18821871598044101,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4415928759","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9856856,0.002982145,0.0086948695,0.0001816324,0.0000073316273,0.000019962394,0.0011135028,0.00008664027,0.001228449],"genre_scores_gemma":[0.97885877,0.001918865,0.014783073,0.000101087906,0.000014925176,0.000013998687,0.0033406129,0.000029826351,0.0009388774],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9999201,0.0000086076125,0.0000055962746,0.000026110303,0.000021646367,0.000017867871],"domain_scores_gemma":[0.9997987,0.000057928497,0.000048575035,0.000017609833,0.000031433603,0.000045653698],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00013016233,0.00025875974,0.0002622693,0.0006999599,0.0001576962,0.00040305484,0.00020331664,0.00029391708,0.00093019113],"category_scores_gemma":[0.00030088215,0.00012510897,0.0002355824,0.00060489384,0.0001727306,0.0006264225,0.00034829514,0.00036725609,0.00033115043],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00018623595,0.0000496015,0.0112075675,0.0002877813,0.000018763925,0.0002505419,0.00026830687,0.0002420091,0.96673256,0.00037742607,0.00008163723,0.020297505],"study_design_scores_gemma":[0.00006345335,0.0009249457,0.5953359,0.00020906395,0.00029218788,0.004999499,0.0025610717,0.010043927,0.35041508,0.0042331074,0.030838277,0.000083486964],"about_ca_topic_score_codex":0.00068251626,"about_ca_topic_score_gemma":0.0012202814,"teacher_disagreement_score":0.00093019113,"about_ca_system_score_codex":0.00020382188,"about_ca_system_score_gemma":0.00034563013,"threshold_uncertainty_score":0.0031117797},"labels":[],"label_agreement":null},{"id":"W4415979618","doi":"10.1099/mgen.0.001726","title":"Multi-omic characterization of the sow colostrum and milk microbiome and proteome","year":2025,"lang":"en","type":"preprint","venue":"Microbial Genomics","topic":"Animal health and immunology","field":"Veterinary","cited_by":0,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Burman University; Agriculture and Agri-Food Canada","funders":"Agriculture and Agri-Food Canada","keywords":"Colostrum; Proteome; Microbiome; Immune system; Metagenomics; Bacteria; Proteomics; Host (biology); Lactation","score_opus":0.03469865363056759,"score_gpt":0.2863275573653978,"score_spread":0.2516289037348302,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4415979618","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.976503,0.0027584666,0.009696224,0.0001397637,0.000043527212,0.000050226285,0.009689665,0.00015987748,0.00095919496],"genre_scores_gemma":[0.95457375,0.0016748009,0.025058713,0.00028610986,0.00003716328,0.00009211229,0.016218197,0.00010493812,0.0019541872],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9998386,0.000015004794,0.000010500318,0.000056301178,0.00005258051,0.000027022463],"domain_scores_gemma":[0.999877,0.00001946801,0.000033238903,0.000011548283,0.00003478915,0.000023931816],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00029350095,0.00045264149,0.00039239923,0.00090137374,0.00026886145,0.0005475009,0.00016792696,0.00026714106,0.0005443248],"category_scores_gemma":[0.0002155193,0.0001754626,0.00042877154,0.00060343236,0.00013257338,0.0002645537,0.00038335737,0.00031725946,0.00026812011],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00006130171,0.000013902212,0.0072567295,0.00006909672,0.000034110304,0.00005218162,0.00002940722,0.00007163679,0.98893857,0.00001797089,0.00007968738,0.0033754716],"study_design_scores_gemma":[0.000012470292,0.0003310733,0.7003221,0.000056500292,0.00022090359,0.00089948555,0.0004035919,0.0069675758,0.2839275,0.00024359734,0.006582098,0.000033055574],"about_ca_topic_score_codex":0.001416962,"about_ca_topic_score_gemma":0.0018212775,"teacher_disagreement_score":0.001416962,"about_ca_system_score_codex":0.00018414557,"about_ca_system_score_gemma":0.00031275264,"threshold_uncertainty_score":0.002817452},"labels":[],"label_agreement":null},{"id":"W4416797650","doi":"10.1099/mgen.0.001572","title":"Global emergence of Acinetobacter baumannii International Clone 12 predominantly found in the Middle East","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Antibiotic Resistance in Bacteria","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Canadian Institute for Advanced Research; Hôpital Charles-Le Moyne; Centre intégré de santé et de services sociaux de Chaudière-Appalaches; Centre Intégré de Santé et de Services Sociaux des Laurentides; Centre Hospitalier Universitaire de Sherbrooke; Université de Sherbrooke","funders":"Umeå Universitet; Fonds de Recherche du Québec - Santé; Vetenskapsrådet; Medicinska fakulteten, Umeå Universitet; Canadian Institute for Advanced Research","keywords":"Middle East; Acinetobacter baumannii; clone (Java method); Whole genome sequencing; Genome; Multilocus sequence typing; Antibiotic resistance; Plasmid; Genotype","score_opus":0.01601729018753794,"score_gpt":0.24867811277480031,"score_spread":0.23266082258726237,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4416797650","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.998422,0.00028710035,0.00024788527,0.000033530894,0.0000073977767,0.00002072863,0.0003768986,0.000017381153,0.00058709504],"genre_scores_gemma":[0.9972057,0.00042564253,0.00060151174,0.000083751176,0.000022679826,0.000016903827,0.0012957252,0.000010336936,0.00033775586],"study_design_codex":"observational","study_design_gemma":"observational","domain_scores_codex":[0.99967015,0.000027081267,0.000029559093,0.0001175195,0.00005945395,0.0000961994],"domain_scores_gemma":[0.9992489,0.000047657555,0.0002976218,0.00006149145,0.00019169507,0.00015255465],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00025431227,0.0003949094,0.00043790985,0.00141396,0.00036479795,0.0010228597,0.0002176687,0.00034893694,0.0012543054],"category_scores_gemma":[0.0006538598,0.00018081453,0.00036891937,0.0016789865,0.00025873852,0.00029108074,0.0006157106,0.0004461497,0.00029217175],"study_design_candidate":"observational","study_design_consensus":"observational","about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00070754264,0.00008376937,0.8788431,0.00013120173,0.00012667147,0.001827616,0.0014564142,0.00011651197,0.087314494,0.00012344058,0.0007026075,0.02856657],"study_design_scores_gemma":[0.000013139131,0.00014955192,0.9875048,0.000032062395,0.0000790722,0.0036348314,0.0011231761,0.00014741515,0.0039278744,0.00003548171,0.0033370187,0.000015573787],"about_ca_topic_score_codex":0.0038349004,"about_ca_topic_score_gemma":0.0028830064,"teacher_disagreement_score":0.0038349004,"about_ca_system_score_codex":0.00024575836,"about_ca_system_score_gemma":0.00028781398,"threshold_uncertainty_score":0.0076251626},"labels":[],"label_agreement":null},{"id":"W4416850537","doi":"10.1099/mgen.0.001739","title":"From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":true,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada; Mitacs","keywords":"Metagenomics; Genome; Reference genome; False positive paradox; Precision and recall; Taxonomic rank; Environmental DNA; Identification (biology)","score_opus":0.036076852098520865,"score_gpt":0.26526806968271366,"score_spread":0.2291912175841928,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4416850537","genre_codex":"methods","genre_gemma":"methods","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"methods","genre_consensus":"methods","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.4803323,0.0034179536,0.48430946,0.0017370064,0.001309413,0.0003931402,0.008875065,0.011750017,0.007875648],"genre_scores_gemma":[0.71821386,0.00040319408,0.26897505,0.0010297066,0.00012836774,0.00016449015,0.009219883,0.0008686741,0.0009967631],"study_design_codex":"design_other","study_design_gemma":"bench_or_experimental","domain_scores_codex":[0.9921239,0.002377378,0.0007534572,0.002131274,0.0021382603,0.00047572097],"domain_scores_gemma":[0.96609336,0.014534352,0.0038863183,0.007697961,0.0071641565,0.0006237409],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.011165257,0.0011001062,0.0009589567,0.0022002398,0.00093834754,0.0031976008,0.0018801928,0.00167362,0.0029715498],"category_scores_gemma":[0.04563977,0.00060493476,0.0014937418,0.0017039687,0.00081107527,0.0021011122,0.0021161523,0.0015747321,0.0032893128],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0034139333,0.000397483,0.35462454,0.0031210892,0.0013929697,0.00082704064,0.0015983084,0.040803254,0.16376418,0.005816536,0.019058252,0.4051824],"study_design_scores_gemma":[0.0002549017,0.0010458401,0.14320605,0.0014830481,0.00060556905,0.0012643031,0.0016444833,0.49812925,0.2880524,0.022470115,0.041511085,0.00033305105],"about_ca_topic_score_codex":0.004210287,"about_ca_topic_score_gemma":0.0062846197,"teacher_disagreement_score":0.011165257,"about_ca_system_score_codex":0.00095539546,"about_ca_system_score_gemma":0.0017461533,"threshold_uncertainty_score":0.059048235},"labels":[],"label_agreement":null},{"id":"W4417437674","doi":"10.1099/mgen.0.001569","title":"Paired-omics-based exploration and characterization of biosynthetic diversity in lichenized fungi","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Lichen and fungal ecology","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":false,"ca_institutions":"University of Manitoba","funders":"Ministero dell’Istruzione, dell’Università e della Ricerca","keywords":"Bioprospecting; Metabolomics; Genome; Metagenomics; Genomics; Gene; Comparative genomics; Drug discovery","score_opus":0.019866375308760235,"score_gpt":0.19277153916974316,"score_spread":0.17290516386098292,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4417437674","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.95725256,0.0026825245,0.018046523,0.00016553377,0.000014768686,0.00007872131,0.019439887,0.00035052755,0.0019690166],"genre_scores_gemma":[0.93243545,0.0016194142,0.043229222,0.0002131412,0.000029669876,0.00011265544,0.021729859,0.00009037524,0.0005402541],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.9995571,0.00006739408,0.000047201316,0.00017721481,0.00009229784,0.00005876854],"domain_scores_gemma":[0.99959284,0.00011521051,0.00011776529,0.000048497364,0.00006707006,0.00005863841],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004930205,0.0006515855,0.00076407206,0.0037186125,0.00059145206,0.0014971815,0.00026780434,0.00047284883,0.0009878442],"category_scores_gemma":[0.0008260994,0.00019428984,0.0008534262,0.0029738094,0.0003327781,0.00074202084,0.00077317347,0.00043854132,0.00045228802],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.00080389524,0.0002095275,0.08648266,0.00084203,0.00033672605,0.0004117092,0.00041195974,0.005500563,0.8516499,0.0005040783,0.00047957088,0.052367393],"study_design_scores_gemma":[0.000079291654,0.000673282,0.71185607,0.0002701206,0.00069679104,0.0017593929,0.0020116426,0.061221004,0.2009739,0.0047360533,0.015574343,0.00014814422],"about_ca_topic_score_codex":0.0012952042,"about_ca_topic_score_gemma":0.0015324303,"teacher_disagreement_score":0.0037186125,"about_ca_system_score_codex":0.00035829554,"about_ca_system_score_gemma":0.00040468608,"threshold_uncertainty_score":0.00330472},"labels":[],"label_agreement":null},{"id":"W4417506982","doi":"10.1099/mgen.0.001575","title":"Sequencing and variant calling of SARS-CoV-2 from floor swabs: a potential tool for identifying emergent lineages","year":2025,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"route_ca_aff":true,"route_ca_fund":false,"route_ca_venue":false,"route_about_ca":true,"ca_institutions":"Ottawa Hospital; NOSM University; Kingston Health Sciences Centre; Queen's University; Sault Area Hospital; University of Ottawa; McGill University; McGill Genome Centre; Sinai Health System; Carleton University; University of Toronto","funders":"","keywords":"Outbreak; Genetic diversity; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Coronavirus disease 2019 (COVID-19); Lineage (genetic); Sampling (signal processing); DNA sequencing","score_opus":0.060828500645749684,"score_gpt":0.3467996864817483,"score_spread":0.2859711858359986,"validation_status":"score_only:v0-immature-baseline","prediction":{"id":"W4417506982","genre_codex":"empirical","genre_gemma":"empirical","domain_codex":null,"domain_gemma":null,"model_version":"metacan-v3-hybrid-931329e0061c","genre_candidate":"empirical","genre_consensus":"empirical","domain_candidate":null,"domain_consensus":null,"prediction_status":"machine_predicted_unvalidated","genre_scores_codex":[0.9381402,0.0014797328,0.04247491,0.00024733227,0.00006941082,0.00022566791,0.012521186,0.00079380354,0.0040476513],"genre_scores_gemma":[0.85064113,0.0009670769,0.12784128,0.00036669883,0.000044271546,0.00013933073,0.016938489,0.000301646,0.0027599786],"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","domain_scores_codex":[0.99914396,0.00012690295,0.00006982841,0.00032790794,0.00025408017,0.000077386976],"domain_scores_gemma":[0.99880743,0.00024417572,0.00031580968,0.000120694196,0.00042012794,0.00009192216],"candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00082528783,0.00045805192,0.00042095908,0.001436986,0.0004707573,0.0009565012,0.00037493536,0.0004530486,0.0010690774],"category_scores_gemma":[0.002076976,0.00028133794,0.00044942123,0.0014857484,0.00029776193,0.00029127728,0.000433703,0.00041026733,0.0007807498],"study_design_candidate":"observational","study_design_consensus":null,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_system_candidate":false,"about_ca_system_consensus":false,"study_design_scores_codex":[0.0006551154,0.0001432969,0.3107448,0.0005014693,0.0002238786,0.0008801379,0.002214146,0.005140715,0.5224464,0.00062624,0.003797472,0.15262637],"study_design_scores_gemma":[0.000057208654,0.0005692981,0.7363596,0.0003598876,0.00028898372,0.0019744083,0.0026795955,0.069090135,0.14832899,0.00173174,0.038385823,0.00017441425],"about_ca_topic_score_codex":0.035893902,"about_ca_topic_score_gemma":0.09232645,"teacher_disagreement_score":0.035893902,"about_ca_system_score_codex":0.00054264016,"about_ca_system_score_gemma":0.0011526226,"threshold_uncertainty_score":0.071370006},"labels":[],"label_agreement":null}]}