{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T22:23:48Z","timestamp":1774650228669,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"D1","funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["89233218CNA000001"],"award-info":[{"award-number":["89233218CNA000001"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC05-00OR22725"],"award-info":[{"award-number":["DE-AC05-00OR22725"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC05-76RL01830"],"award-info":[{"award-number":["DE-AC05-76RL01830"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Genomes OnLine Database (GOLD) (https:\/\/gold.jgi.doe.gov\/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world. The current version of the database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) and Analysis Projects (283 481). These four levels contain over 600 metadata fields, which includes 76 controlled vocabulary (CV) tables containing 3873 terms. GOLD provides an interactive web user interface for browsing and searching by a wide range of project and metadata fields. Users can enter details about their own projects in GOLD, which acts as a gatekeeper to ensure that metadata is accurately documented before submitting sequence information to the Integrated Microbial Genomes (IMG) system for analysis. In order to maintain a reference dataset for use by members of the scientific community, GOLD also imports projects from public repositories such as GenBank and SRA. The current status of the database, along with recent updates and improvements are described in this manuscript.<\/jats:p>","DOI":"10.1093\/nar\/gkaa983","type":"journal-article","created":{"date-parts":[[2020,10,19]],"date-time":"2020-10-19T15:21:37Z","timestamp":1603120897000},"page":"D723-D733","source":"Crossref","is-referenced-by-count":187,"title":["Genomes OnLine Database (GOLD) v.8: overview and updates"],"prefix":"10.1093","volume":"49","author":[{"given":"Supratim","family":"Mukherjee","sequence":"first","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Dimitri","family":"Stamatis","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Jon","family":"Bertsch","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Galina","family":"Ovchinnikova","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6670-9157","authenticated-orcid":false,"given":"Jagadish\u00a0Chandrabose","family":"Sundaramurthi","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Janey","family":"Lee","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Mahathi","family":"Kandimalla","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2026-9798","authenticated-orcid":false,"given":"I-Min A","family":"Chen","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"given":"Nikos C","family":"Kyrpides","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0871-5567","authenticated-orcid":false,"given":"T B K","family":"Reddy","sequence":"additional","affiliation":[{"name":"DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,11,5]]},"reference":[{"key":"2021010313122132400_B1","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol."},{"key":"2021010313122132400_B2","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1186\/s40168-018-0550-0","article-title":"Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes","volume":"6","author":"Alneberg","year":"2018","journal-title":"Microbiome"},{"key":"2021010313122132400_B3","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1038\/s41587-020-0501-8","article-title":"A complete domain-to-species taxonomy for Bacteria and Archaea","volume":"38","author":"Parks","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"2021010313122132400_B4","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1038\/s41564-020-0733-x","article-title":"Roadmap for naming uncultivated Archaea and Bacteria","volume":"5","author":"Murray","year":"2020","journal-title":"Nat. Microbiol."},{"key":"2021010313122132400_B5","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41597-020-0497-4","article-title":"A synthesis of bacterial and archaeal phenotypic trait data","volume":"7","author":"Madin","year":"2020","journal-title":"Sci. Data"},{"key":"2021010313122132400_B6","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/bioinformatics\/15.9.773","article-title":"Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide","volume":"15","author":"Kyrpides","year":"1999","journal-title":"Bioinformatics"},{"key":"2021010313122132400_B7","doi-asserted-by":"crossref","first-page":"D446","DOI":"10.1093\/nar\/gkw992","article-title":"Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements","volume":"45","author":"Mukherjee","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B8","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gky977","article-title":"Genomes OnLine database (GOLD) v.7: updates and new features","volume":"47","author":"Mukherjee","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B9","doi-asserted-by":"crossref","first-page":"D1099","DOI":"10.1093\/nar\/gku950","article-title":"The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification","volume":"43","author":"Reddy","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B10","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s12915-019-0661-5","article-title":"A global survey of arsenic-related genes in soil microbiomes","volume":"17","author":"Dunivin","year":"2019","journal-title":"BMC Biol."},{"key":"2021010313122132400_B11","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/s41467-019-08377-w","article-title":"Trait-based community assembly and succession of the infant gut microbiome","volume":"10","author":"Guittar","year":"2019","journal-title":"Nat. Commun."},{"key":"2021010313122132400_B12","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nbt1360","article-title":"The minimum information about a genome sequence (MIGS) specification","volume":"26","author":"Field","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2021010313122132400_B13","doi-asserted-by":"crossref","first-page":"599","DOI":"10.4056\/sigs.5559608","article-title":"Genomic standards consortium projects","volume":"9","author":"Field","year":"2014","journal-title":"Stand. Genomic Sci."},{"key":"2021010313122132400_B14","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/2041-1480-4-43","article-title":"The environment ontology: contextualising biological and biomedical entities","volume":"4","author":"Buttigieg","year":"2013","journal-title":"J. Biomed. Semant."},{"key":"2021010313122132400_B15","doi-asserted-by":"crossref","first-page":"D67","DOI":"10.1093\/nar\/gkv1276","article-title":"GenBank","volume":"44","author":"Clark","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B16","doi-asserted-by":"crossref","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B17","doi-asserted-by":"crossref","first-page":"D666","DOI":"10.1093\/nar\/gky901","article-title":"IMG\/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes","volume":"47","author":"Chen","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B18","doi-asserted-by":"crossref","first-page":"D507","DOI":"10.1093\/nar\/gkw929","article-title":"IMG\/M: integrated genome and metagenome comparative data analysis system","volume":"45","author":"Chen","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B19","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/s40793-015-0077-y","article-title":"The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)","volume":"10","author":"Huntemann","year":"2015","journal-title":"Stand. Genomic Sci."},{"key":"2021010313122132400_B20","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI Taxonomy database","volume":"40","author":"Federhen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2021010313122132400_B21","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.syapm.2018.07.003","article-title":"The importance of designating type material for uncultured taxa","volume":"42","author":"Chuvochina","year":"2019","journal-title":"Syst. Appl. Microbiol."},{"key":"2021010313122132400_B22","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1038\/ismej.2017.113","article-title":"Uncultivated microbes in need of their own taxonomy","volume":"11","author":"Konstantinidis","year":"2017","journal-title":"ISME J"},{"key":"2021010313122132400_B23","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/s41597-020-0524-5","article-title":"COVID-19 pandemic reveals the peril of ignoring metadata standards","volume":"7","author":"Schriml","year":"2020","journal-title":"Sci. Data"},{"key":"2021010313122132400_B24","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.1111\/j.1462-2920.2010.02270.x","article-title":"A call for standardized classification of metagenome projects","volume":"12","author":"Ivanova","year":"2010","journal-title":"Environ. Microbiol."},{"key":"2021010313122132400_B25","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"2021010313122132400_B26","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/s41579-020-0377-0","article-title":"The National Microbiome Data Collaborative: enabling microbiome science","volume":"18","author":"Wood-Charlson","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"2021010313122132400_B27","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nbt.1823","article-title":"Minimum information about a marker gene sequence (MIMARKS) and minimum information about any sequence (MIxS) specifications","volume":"29","author":"Yilmaz","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2021010313122132400_B28","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1016\/j.csbj.2020.07.020","article-title":"Method development for cross-study microbiome data mining: challenges and opportunities","volume":"18","author":"Su","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/D1\/D723\/35364452\/gkaa983.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/D1\/D723\/35364452\/gkaa983.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,3]],"date-time":"2021-01-03T18:15:28Z","timestamp":1609697728000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D723\/5957166"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,5]]},"references-count":28,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2020,11,5]]},"published-print":{"date-parts":[[2021,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa983","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,1,8]]},"published":{"date-parts":[[2020,11,5]]}}}