{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T12:39:23Z","timestamp":1771072763502,"version":"3.50.1"},"reference-count":49,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,10,24]],"date-time":"2019-10-24T00:00:00Z","timestamp":1571875200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["2013-67015-21202"],"award-info":[{"award-number":["2013-67015-21202"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011102","name":"Seventh Framework Programme","doi-asserted-by":"publisher","award":["613689"],"award-info":[{"award-number":["613689"]}],"id":[{"id":"10.13039\/100011102","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Bovine Genome Database (BGD) (http:\/\/bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.<\/jats:p>","DOI":"10.1093\/nar\/gkz944","type":"journal-article","created":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T23:28:43Z","timestamp":1570577323000},"source":"Crossref","is-referenced-by-count":16,"title":["Bovine Genome Database: new annotation tools for a new reference genome"],"prefix":"10.1093","author":[{"given":"Md","family":"Shamimuzzaman","sequence":"first","affiliation":[{"name":"Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin J","family":"Le\u00a0Tourneau","sequence":"additional","affiliation":[{"name":"Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deepak R","family":"Unni","sequence":"additional","affiliation":[{"name":"Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94608, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colin M","family":"Diesh","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deborah A","family":"Triant","sequence":"additional","affiliation":[{"name":"Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy T","family":"Walsh","sequence":"additional","affiliation":[{"name":"Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aditi","family":"Tayal","sequence":"additional","affiliation":[{"name":"Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gavin C","family":"Conant","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA"},{"name":"Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA"},{"name":"Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8295-020X","authenticated-orcid":false,"given":"Darren E","family":"Hagen","sequence":"additional","affiliation":[{"name":"Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4248-7713","authenticated-orcid":false,"given":"Christine G","family":"Elsik","sequence":"additional","affiliation":[{"name":"Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA"},{"name":"Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA"},{"name":"MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,24]]},"reference":[{"key":"2019102405395085800_B1","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1038\/s41576-018-0082-2","article-title":"Harnessing genomic information for livestock improvement","volume":"20","author":"Georges","year":"2019","journal-title":"Nat. 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