Expanded and updated data and a query pipeline for iBeetle-Base
Abstract The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compare...
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| Veröffentlicht in: | Nucleic acids research 2018-01, Vol.46 (D1), p.D831-D835 |
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| container_title | Nucleic acids research |
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| creator | Dönitz, Jürgen Gerischer, Lizzy Hahnke, Stefan Pfeiffer, Stefan Bucher, Gregor |
| description | Abstract
The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/ |
| doi_str_mv | 10.1093/nar/gkx984 |
| format | Article |
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The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkx984</identifier><identifier>PMID: 29069517</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Animals ; Database Issue ; Databases, Genetic ; Gene Ontology ; Phenotype ; RNA Interference ; Tribolium - genetics ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2018-01, Vol.46 (D1), p.D831-D835</ispartof><rights>The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018</rights><rights>The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c408t-f94dc7182eb6a3b9afc01dd7d33530ae8b265d18b577cf2d1feb20baeff182483</citedby><cites>FETCH-LOGICAL-c408t-f94dc7182eb6a3b9afc01dd7d33530ae8b265d18b577cf2d1feb20baeff182483</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753255/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753255/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29069517$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dönitz, Jürgen</creatorcontrib><creatorcontrib>Gerischer, Lizzy</creatorcontrib><creatorcontrib>Hahnke, Stefan</creatorcontrib><creatorcontrib>Pfeiffer, Stefan</creatorcontrib><creatorcontrib>Bucher, Gregor</creatorcontrib><title>Expanded and updated data and a query pipeline for iBeetle-Base</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/</description><subject>Animals</subject><subject>Database Issue</subject><subject>Databases, Genetic</subject><subject>Gene Ontology</subject><subject>Phenotype</subject><subject>RNA Interference</subject><subject>Tribolium - genetics</subject><subject>User-Computer Interface</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kMtOwzAQRS0EouWx4QNQNkgIKdSPOLE3IFqVh1SJDawtJx6XQJoEO0Ht32NoqWDDZmbkOXM9cxE6IfiSYMlGtXaj-dtSimQHDQlLaZzIlO6iIWaYxwQnYoAOvH_FmCSEJ_toQCVOJSfZEF1Pl62uDZgoxKhvje5CHaL-ftDRew9uFbVlC1VZQ2QbF5VjgK6CeKw9HKE9qysPx5t8iJ5vp0-T-3j2ePcwuZnFRYJFF1uZmCIjgkKeapZLbQtMjMkMY5xhDSKnKTdE5DzLCksNsZBTnGuwNgwlgh2iq7Vu2-cLMAXUndOVal250G6lGl2qv526fFHz5kPxjDPKeRA43wi4JtzkO7UofQFVpWtoeq-I5CmWghAc0Is1WrjGewd2-w3B6stxFRxXa8cDfPp7sS36Y3EAztZA07f_CX0Cf6SK1A</recordid><startdate>20180104</startdate><enddate>20180104</enddate><creator>Dönitz, Jürgen</creator><creator>Gerischer, Lizzy</creator><creator>Hahnke, Stefan</creator><creator>Pfeiffer, Stefan</creator><creator>Bucher, Gregor</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></search><sort><creationdate>20180104</creationdate><title>Expanded and updated data and a query pipeline for iBeetle-Base</title><author>Dönitz, Jürgen ; Gerischer, Lizzy ; Hahnke, Stefan ; Pfeiffer, Stefan ; Bucher, Gregor</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c408t-f94dc7182eb6a3b9afc01dd7d33530ae8b265d18b577cf2d1feb20baeff182483</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Animals</topic><topic>Database Issue</topic><topic>Databases, Genetic</topic><topic>Gene Ontology</topic><topic>Phenotype</topic><topic>RNA Interference</topic><topic>Tribolium - genetics</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dönitz, Jürgen</creatorcontrib><creatorcontrib>Gerischer, Lizzy</creatorcontrib><creatorcontrib>Hahnke, Stefan</creatorcontrib><creatorcontrib>Pfeiffer, Stefan</creatorcontrib><creatorcontrib>Bucher, Gregor</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>Dönitz, Jürgen</au><au>Gerischer, Lizzy</au><au>Hahnke, Stefan</au><au>Pfeiffer, Stefan</au><au>Bucher, Gregor</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Expanded and updated data and a query pipeline for iBeetle-Base</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2018-01-04</date><risdate>2018</risdate><volume>46</volume><issue>D1</issue><spage>D831</spage><epage>D835</epage><pages>D831-D835</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29069517</pmid><doi>10.1093/nar/gkx984</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2018-01, Vol.46 (D1), p.D831-D835 |
| issn | 0305-1048 1362-4962 |
| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Database Issue Databases, Genetic Gene Ontology Phenotype RNA Interference Tribolium - genetics User-Computer Interface |
| title | Expanded and updated data and a query pipeline for iBeetle-Base |
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