The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources
Abstract The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene f...
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| Veröffentlicht in: | Nucleic acids research 2019-01, Vol.47 (D1), p.D867-D873 |
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| creator | Ruzicka, Leyla Howe, Douglas G Ramachandran, Sridhar Toro, Sabrina Van Slyke, Ceri E Bradford, Yvonne M Eagle, Anne Fashena, David Frazer, Ken Kalita, Patrick Mani, Prita Martin, Ryan Moxon, Sierra Taylor Paddock, Holly Pich, Christian Schaper, Kevin Shao, Xiang Singer, Amy Westerfield, Monte |
| description | Abstract
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research. |
| doi_str_mv | 10.1093/nar/gky1090 |
| format | Article |
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The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gky1090</identifier><identifier>PMID: 30407545</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Database Issue ; Databases, Genetic ; Gene Expression - genetics ; Gene Ontology ; Genome - genetics ; Genomics ; Humans ; Molecular Sequence Annotation ; Mutation - genetics ; Phenotype ; Zebrafish - genetics</subject><ispartof>Nucleic acids research, 2019-01, Vol.47 (D1), p.D867-D873</ispartof><rights>The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c412t-9ffd264cce0c7c5dea70367272aca18d99698ec55b8b286d8fb863f5061993ac3</citedby><cites>FETCH-LOGICAL-c412t-9ffd264cce0c7c5dea70367272aca18d99698ec55b8b286d8fb863f5061993ac3</cites><orcidid>0000-0002-1009-339X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323962/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323962/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30407545$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ruzicka, Leyla</creatorcontrib><creatorcontrib>Howe, Douglas G</creatorcontrib><creatorcontrib>Ramachandran, Sridhar</creatorcontrib><creatorcontrib>Toro, Sabrina</creatorcontrib><creatorcontrib>Van Slyke, Ceri E</creatorcontrib><creatorcontrib>Bradford, Yvonne M</creatorcontrib><creatorcontrib>Eagle, Anne</creatorcontrib><creatorcontrib>Fashena, David</creatorcontrib><creatorcontrib>Frazer, Ken</creatorcontrib><creatorcontrib>Kalita, Patrick</creatorcontrib><creatorcontrib>Mani, Prita</creatorcontrib><creatorcontrib>Martin, Ryan</creatorcontrib><creatorcontrib>Moxon, Sierra Taylor</creatorcontrib><creatorcontrib>Paddock, Holly</creatorcontrib><creatorcontrib>Pich, Christian</creatorcontrib><creatorcontrib>Schaper, Kevin</creatorcontrib><creatorcontrib>Shao, Xiang</creatorcontrib><creatorcontrib>Singer, Amy</creatorcontrib><creatorcontrib>Westerfield, Monte</creatorcontrib><title>The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.</description><subject>Animals</subject><subject>Database Issue</subject><subject>Databases, Genetic</subject><subject>Gene Expression - genetics</subject><subject>Gene Ontology</subject><subject>Genome - genetics</subject><subject>Genomics</subject><subject>Humans</subject><subject>Molecular Sequence Annotation</subject><subject>Mutation - genetics</subject><subject>Phenotype</subject><subject>Zebrafish - genetics</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kU1v1DAQhi0EotvCiTvyCSG1of6Kk3BAqioolSoqVe2Fi-U446xpYqd2QrV_gV-N210quHCaGc2jZyy_CL2h5AMlDT_2Oh73t5vck2doRblkhWgke45WhJOyoETUe2g_pR-EUEFL8RLtcSJIVYpyhX5drwF_hzZq69Ian3sb4qhnFzz-BvN9iLcfsYd7nJZpCnHGeY198IUJnfM97sFDOsLRmTVEfJYnfOnnMIR-g7X3YX5Updx3eM6XTobBaW8AB_tAhxHwFaSwRAPpFXph9ZDg9a4eoJsvn69PvxYXl2fnpycXhRGUzUVjbcekMAaIqUzZga4IlxWrmDaa1l3TyKYGU5Zt3bJadrVta8ltSSRtGq4NP0Cftt5paUfoDPg56kFN0Y06blTQTv278W6t-vBTSc54_tgseL8TxHC3QJrV6JKBYdAewpIUo5wyXlVEZPRwi5oYUopgn85Qoh7SUzk9tUsv02__ftkT-yeuDLzbAmGZ_mv6DUPOpxA</recordid><startdate>20190108</startdate><enddate>20190108</enddate><creator>Ruzicka, Leyla</creator><creator>Howe, Douglas G</creator><creator>Ramachandran, Sridhar</creator><creator>Toro, Sabrina</creator><creator>Van Slyke, Ceri E</creator><creator>Bradford, Yvonne M</creator><creator>Eagle, Anne</creator><creator>Fashena, David</creator><creator>Frazer, Ken</creator><creator>Kalita, Patrick</creator><creator>Mani, Prita</creator><creator>Martin, Ryan</creator><creator>Moxon, Sierra Taylor</creator><creator>Paddock, Holly</creator><creator>Pich, Christian</creator><creator>Schaper, Kevin</creator><creator>Shao, Xiang</creator><creator>Singer, Amy</creator><creator>Westerfield, Monte</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-1009-339X</orcidid></search><sort><creationdate>20190108</creationdate><title>The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources</title><author>Ruzicka, Leyla ; Howe, Douglas G ; Ramachandran, Sridhar ; Toro, Sabrina ; Van Slyke, Ceri E ; Bradford, Yvonne M ; Eagle, Anne ; Fashena, David ; Frazer, Ken ; Kalita, Patrick ; Mani, Prita ; Martin, Ryan ; Moxon, Sierra Taylor ; Paddock, Holly ; Pich, Christian ; Schaper, Kevin ; Shao, Xiang ; Singer, Amy ; Westerfield, Monte</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-9ffd264cce0c7c5dea70367272aca18d99698ec55b8b286d8fb863f5061993ac3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Animals</topic><topic>Database Issue</topic><topic>Databases, Genetic</topic><topic>Gene Expression - genetics</topic><topic>Gene Ontology</topic><topic>Genome - genetics</topic><topic>Genomics</topic><topic>Humans</topic><topic>Molecular Sequence Annotation</topic><topic>Mutation - genetics</topic><topic>Phenotype</topic><topic>Zebrafish - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ruzicka, Leyla</creatorcontrib><creatorcontrib>Howe, Douglas G</creatorcontrib><creatorcontrib>Ramachandran, Sridhar</creatorcontrib><creatorcontrib>Toro, Sabrina</creatorcontrib><creatorcontrib>Van Slyke, Ceri E</creatorcontrib><creatorcontrib>Bradford, Yvonne M</creatorcontrib><creatorcontrib>Eagle, Anne</creatorcontrib><creatorcontrib>Fashena, David</creatorcontrib><creatorcontrib>Frazer, Ken</creatorcontrib><creatorcontrib>Kalita, Patrick</creatorcontrib><creatorcontrib>Mani, Prita</creatorcontrib><creatorcontrib>Martin, Ryan</creatorcontrib><creatorcontrib>Moxon, Sierra Taylor</creatorcontrib><creatorcontrib>Paddock, Holly</creatorcontrib><creatorcontrib>Pich, Christian</creatorcontrib><creatorcontrib>Schaper, Kevin</creatorcontrib><creatorcontrib>Shao, Xiang</creatorcontrib><creatorcontrib>Singer, Amy</creatorcontrib><creatorcontrib>Westerfield, Monte</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ruzicka, Leyla</au><au>Howe, Douglas G</au><au>Ramachandran, Sridhar</au><au>Toro, Sabrina</au><au>Van Slyke, Ceri E</au><au>Bradford, Yvonne M</au><au>Eagle, Anne</au><au>Fashena, David</au><au>Frazer, Ken</au><au>Kalita, Patrick</au><au>Mani, Prita</au><au>Martin, Ryan</au><au>Moxon, Sierra Taylor</au><au>Paddock, Holly</au><au>Pich, Christian</au><au>Schaper, Kevin</au><au>Shao, Xiang</au><au>Singer, Amy</au><au>Westerfield, Monte</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2019-01-08</date><risdate>2019</risdate><volume>47</volume><issue>D1</issue><spage>D867</spage><epage>D873</epage><pages>D867-D873</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagents. New features at ZFIN include increased support for genomic regions and for non-coding genes, and support for more expressive Gene Ontology annotations. ZFIN has recently taken over maintenance of the zebrafish reference genome sequence as part of the Genome Reference Consortium. ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO). The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>30407545</pmid><doi>10.1093/nar/gky1090</doi><orcidid>https://orcid.org/0000-0002-1009-339X</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Nucleic acids research, 2019-01, Vol.47 (D1), p.D867-D873 |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Database Issue Databases, Genetic Gene Expression - genetics Gene Ontology Genome - genetics Genomics Humans Molecular Sequence Annotation Mutation - genetics Phenotype Zebrafish - genetics |
| title | The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources |
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