{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T19:02:06Z","timestamp":1784314926997,"version":"3.55.0"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,21]],"date-time":"2022-11-21T00:00:00Z","timestamp":1668988800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019573","name":"Amsterdam UMC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019573","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["205321_184955"],"award-info":[{"award-number":["205321_184955"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NCCR Microbiomes","award":["51NF40_180575"],"award-info":[{"award-number":["51NF40_180575"]}]},{"name":"German Federal Ministry of Education and Research","award":["031A537B"],"award-info":[{"award-number":["031A537B"]}]},{"name":"German Federal Ministry of Education and Research","award":["031L0181A"],"award-info":[{"award-number":["031L0181A"]}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["395357507"],"award-info":[{"award-number":["395357507"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["NFDI4Microbiota"],"award-info":[{"award-number":["NFDI4Microbiota"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Grant","award":["PGC2018-098073-A-I00"],"award-info":[{"award-number":["PGC2018-098073-A-I00"]}]},{"name":"European Grant","award":["MCIU\/AEI\/FEDER"],"award-info":[{"award-number":["MCIU\/AEI\/FEDER"]}]},{"name":"Spanish Ministry of Universities","award":["FPU-19\/06635"],"award-info":[{"award-number":["FPU-19\/06635"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The interpretation of genomic, transcriptomic and other microbial \u2018omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http:\/\/progenomes.embl.de\/<\/jats:p>","DOI":"10.1093\/nar\/gkac1078","type":"journal-article","created":{"date-parts":[[2022,11,21]],"date-time":"2022-11-21T11:51:13Z","timestamp":1669031473000},"page":"D760-D766","source":"Crossref","is-referenced-by-count":78,"title":["proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0884-8124","authenticated-orcid":false,"given":"Anthony","family":"Fullam","sequence":"first","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3560-4288","authenticated-orcid":false,"given":"Ivica","family":"Letunic","sequence":"additional","affiliation":[{"name":"Biobyte solutions GmbH , Bothestr. 142, 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8587-4177","authenticated-orcid":false,"given":"Thomas S B","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7077-2127","authenticated-orcid":false,"given":"Quinten R","family":"Ducarmon","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7894-8182","authenticated-orcid":false,"given":"Nicolai","family":"Karcher","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6606-2202","authenticated-orcid":false,"given":"Supriya","family":"Khedkar","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2841-872X","authenticated-orcid":false,"given":"Michael","family":"Kuhn","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3947-4444","authenticated-orcid":false,"given":"Martin","family":"Larralde","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, European Molecular Biology Laboratory , 69117 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1961-7548","authenticated-orcid":false,"given":"Oleksandr\u00a0M","family":"Maistrenko","sequence":"additional","affiliation":[{"name":"Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology & Biogeochemistry , 1797 SZ, \u2019t Horntje (Texel), Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5697-2007","authenticated-orcid":false,"given":"Lukas","family":"Malfertheiner","sequence":"additional","affiliation":[{"name":"Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich , 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7050-2239","authenticated-orcid":false,"given":"Alessio","family":"Milanese","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, Department of Biology and Swiss Institute of Bioinformatics , ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8413-9920","authenticated-orcid":false,"given":"Joao\u00a0Frederico\u00a0Matias","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich , 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8206-1565","authenticated-orcid":false,"given":"Claudia","family":"Sanchis-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - 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