The generic genome browser: a building block for a model organism system database
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user...
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| Veröffentlicht in: | Genome research 2002-10, Vol.12 (10), p.1599-1610 |
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| container_title | Genome research |
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| creator | Stein, Lincoln D Mungall, Christopher Shu, ShengQiang Caudy, Michael Mangone, Marco Day, Allen Nickerson, Elizabeth Stajich, Jason E Harris, Todd W Arva, Adrian Lewis, Suzanna |
| description | The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org. |
| doi_str_mv | 10.1101/gr.403602 |
| format | Article |
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In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. 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In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.</description><subject>Animals</subject><subject>Computer Graphics</subject><subject>Database Management Systems - trends</subject><subject>Databases, Genetic</subject><subject>Diptera - genetics</subject><subject>Drosophila melanogaster - genetics</subject><subject>Drosophila Proteins - genetics</subject><subject>Genome</subject><subject>Resources</subject><subject>Transcription Factors - genetics</subject><issn>1088-9051</issn><issn>1054-9803</issn><issn>1549-5469</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1Lw0AQhhdRtFYP_gHZk-AhdfYr3QgeRPyCggj1vGw2kxhNsnU3Vfz3prT4cfI0w8zzDu_wEnLEYMIYsLMqTCSIFPgWGTEls0TJNNseetA6yUCxPbIf4wsACKn1LtljXKSaKzEij_NnpBV2GGq3qr5Fmgf_ETGcU0vzZd0UdVfRvPHulZY-DMPWF9hQHyrb1bGl8TP22NLC9ja3EQ_ITmmbiIebOiZPN9fzq7tk9nB7f3U5S9xgrk8cFkpLQKVB2xJ5mgnJpkpxLoRL1WCal6BSKWzhOExlwfM8dYDDEzLnCGJMLtZ3F8u8xcJh1wfbmEWoWxs-jbe1-bvp6mdT-XfD9FQJNehPNvrg35YYe9PW0WHT2A79MpopZypTKvsXZFqBTAUfwNM16IKPMWD5bYaBWQVlqmDWQQ3s8W_3P-QmGfEFHq2N4A</recordid><startdate>200210</startdate><enddate>200210</enddate><creator>Stein, Lincoln D</creator><creator>Mungall, Christopher</creator><creator>Shu, ShengQiang</creator><creator>Caudy, Michael</creator><creator>Mangone, Marco</creator><creator>Day, Allen</creator><creator>Nickerson, Elizabeth</creator><creator>Stajich, Jason E</creator><creator>Harris, Todd W</creator><creator>Arva, Adrian</creator><creator>Lewis, Suzanna</creator><general>Cold Spring Harbor Laboratory Press</general><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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>200210</creationdate><title>The generic genome browser: a building block for a model organism system database</title><author>Stein, Lincoln D ; Mungall, Christopher ; Shu, ShengQiang ; Caudy, Michael ; Mangone, Marco ; Day, Allen ; Nickerson, Elizabeth ; Stajich, Jason E ; Harris, Todd W ; Arva, Adrian ; Lewis, Suzanna</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c469t-ced5840e5808afe2693417552233c650512f05643adc2074d2bb6c0e0004b2e03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>Animals</topic><topic>Computer Graphics</topic><topic>Database Management Systems - trends</topic><topic>Databases, Genetic</topic><topic>Diptera - genetics</topic><topic>Drosophila melanogaster - genetics</topic><topic>Drosophila Proteins - genetics</topic><topic>Genome</topic><topic>Resources</topic><topic>Transcription Factors - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Stein, Lincoln D</creatorcontrib><creatorcontrib>Mungall, Christopher</creatorcontrib><creatorcontrib>Shu, ShengQiang</creatorcontrib><creatorcontrib>Caudy, Michael</creatorcontrib><creatorcontrib>Mangone, Marco</creatorcontrib><creatorcontrib>Day, Allen</creatorcontrib><creatorcontrib>Nickerson, Elizabeth</creatorcontrib><creatorcontrib>Stajich, Jason E</creatorcontrib><creatorcontrib>Harris, Todd W</creatorcontrib><creatorcontrib>Arva, Adrian</creatorcontrib><creatorcontrib>Lewis, Suzanna</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Stein, Lincoln D</au><au>Mungall, Christopher</au><au>Shu, ShengQiang</au><au>Caudy, Michael</au><au>Mangone, Marco</au><au>Day, Allen</au><au>Nickerson, Elizabeth</au><au>Stajich, Jason E</au><au>Harris, Todd W</au><au>Arva, Adrian</au><au>Lewis, Suzanna</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The generic genome browser: a building block for a model organism system database</atitle><jtitle>Genome research</jtitle><addtitle>Genome Res</addtitle><date>2002-10</date><risdate>2002</risdate><volume>12</volume><issue>10</issue><spage>1599</spage><epage>1610</epage><pages>1599-1610</pages><issn>1088-9051</issn><issn>1054-9803</issn><eissn>1549-5469</eissn><abstract>The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.</abstract><cop>United States</cop><pub>Cold Spring Harbor Laboratory Press</pub><pmid>12368253</pmid><doi>10.1101/gr.403602</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Genome research, 2002-10, Vol.12 (10), p.1599-1610 |
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| language | eng |
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| source | MEDLINE; PubMed Central; Alma/SFX Local Collection |
| subjects | Animals Computer Graphics Database Management Systems - trends Databases, Genetic Diptera - genetics Drosophila melanogaster - genetics Drosophila Proteins - genetics Genome Resources Transcription Factors - genetics |
| title | The generic genome browser: a building block for a model organism system database |
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