{"id":"W3104596207","doi":"10.1038/s41587-020-0718-6","title":"A genomic catalog of Earth’s microbiomes","year":2020,"lang":"en","type":"article","venue":"Nature Biotechnology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":973,"is_retracted":false,"has_abstract":true,"ca_institutions":"Concordia University; University of Windsor; University of Waterloo; Geological Survey of Canada; Natural Resources Canada; University of Calgary; Agriculture and Agri-Food Canada; University of British Columbia; Institut National de la Recherche Scientifique; University of Toronto; McMaster University","funders":"Lawrence Livermore National Laboratory; Mikrobiologický Ústav, Akademie Věd České Republiky; Agriculture and Agri-Food Canada; Sandia National Laboratories; Great Lakes Bioenergy Research Center; Natural Resources Canada; School of Life Sciences, Arizona State University; University of Oregon; Advanced Research Projects Agency - Energy; Stockholms Universitet; College of Engineering, Michigan State University; Addis Ababa University; North Carolina State University; University of Washington; Linnéuniversitetet; Universidad de Buenos Aires; Office of Science; Max-Planck-Institut für Terrestrische Mikrobiologie; Akademie Věd České Republiky; Universität Wien; Georgia Institute of Technology; Consejo Nacional de Investigaciones Científicas y Técnicas; Baqiyatallah University of Medical Sciences; University of Toronto; University of New South Wales; National Energy Research Scientific Computing Center; Directorate for Biological Sciences; Joint Genome Institute; University of Waikato; Oregon State University; Montana State University; Koninklijk Nederlands Instituut voor Onderzoek der Zee; West Virginia University; University of California, San Diego; University of Montana; University of Arkansas for Medical Sciences; Pennsylvania State University; Michigan State University; McMaster University; University of California, Davis; University of Akron; Harvard University; Science for Life Laboratory; Universiteit Utrecht; University of Minnesota; Oklahoma State University; AgResearch; Arizona State University; Division of Ocean Sciences; University of Wisconsin-Madison; U.S. Department of Energy; Sveriges Lantbruksuniversitet; Lembaga Ilmu Pengetahuan Indonesia; Aarhus Universitet; Ohio State University; Clemson University; Louisiana State University; Colorado State University","keywords":"Metagenomics; Biology; Microbiome; Phylum; Genome; Microbial ecology; Archaea; Evolutionary biology; Ecology; Computational biology; Phylogenetic tree; Extant taxon; Host (biology); Bacteria; Gene; Genetics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00003952496,0.0001309307,0.0001862987,0.00004735869,0.00003252771,0.000003331043,0.0002957752,0.0007689761,0.000007557383],"category_scores_gemma":[0.00007112006,0.0001231849,0.0000810009,0.0001290959,0.000181779,2.456062e-7,0.0002777269,0.0002225329,0.00001244079],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000002589658,"about_ca_system_score_gemma":0.00003975974,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006852561,"about_ca_topic_score_gemma":0.00001568996,"domain_scores_codex":[0.9992759,0.00001313367,0.0001588254,0.0003289541,0.00004127753,0.0001818837],"domain_scores_gemma":[0.9995548,0.000005247093,0.00007719862,0.0002784388,0.00004378767,0.00004053786],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0000372336,0.00001480638,0.001112236,0.00001533434,0.00007285949,0.000001779574,0.00003720826,0.000003836548,0.99539,0.0005910642,0.001538865,0.001184781],"study_design_scores_gemma":[0.0002439156,0.0002545067,0.003311249,0.000001825696,0.0000114941,0.00001143293,0.00003985309,0.000003744322,0.7903641,0.0000621112,0.2055876,0.0001081946],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9820021,0.01365206,0.0001223132,0.003630155,0.0001359922,0.0001243715,0.00008416785,0.00001236043,0.0002364167],"genre_scores_gemma":[0.995939,0.0007892837,0.002108867,0.0009390063,0.0001240041,0.000004411446,0.00003864822,0.00001617386,0.00004061349],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2050259,"threshold_uncertainty_score":0.5931048,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005294096201759396,"score_gpt":0.2089388733343887,"score_spread":0.2036447771326293,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}